Process and Microorganisms for Production of Lipids

ABSTRACT

The present invention provides a process for producing lipids for biofuel or lubricant and  Streptomyces  bacteria used in the process. The process comprises cultivating bacterial cells of the genus  Streptomyces  in a medium comprising organic waste(s) or residue(s) or mixtures thereof as carbon and/or nutrient source(s), recovering lipids from the cells of said bacteria or from the cultivation medium, and using the recovered lipids or a fraction thereof as biofuel and/or lubricant, or as a starting material for biofuel and/or lubricant production. 
     In addition, in one aspect the invention provides products obtained by using the process according to this disclosure.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application claims the benefit under 35 U.S.C. §119(e) toU.S. Provisional Application No. 61/347,913, the content of which isincorporated herein by reference in its entirety.

FIELD OF THE INVENTION

The present invention relates to a process for producing lipids forbiofuel or lubricant applications and microbial strains useable in theprocess.

BACKGROUND OF THE INVENTION

The use of renewable biological material for the production of biofuelsis generally motivated by decreasing climate change impacts, by securingthe supply of fuels and by economic factors. However, the use of ediblecrops to create fuels instead of further refining them to food forincreasing human population is more and more ethically short-lived.Therefore, biological sources that cannot be used for feeding of peopleor cattle and that can be manufactured in environmentally friendlymanner, are of growing interest.

BCC Research (http://www.bccresearch.com/) estimates that the globalmarket for liquid biofuels was worth $30.3 billion in 2008. This shouldincrease to $42.8 billion in 2013, for a compound annual growth rate(CAGB) of 7.2%. Another perspective to the market is the volume. In 2008biofuel production capacity across the 21 countries considered in thestudy report of European Union totaled 10.9 billion litres of biodiesel,and 66.6 billion litres of bioethanol. Over 99% of this production isconsidered as so called 1st generation biofuel, including both sugar andstarch based bioethanol, and oilseed and waste oil based biodiesel.Biodiesel can be made from oilseed crops, animal fats or from recycledgreases. Since it is known that algae and some microorganisms arecapable of producing and/or accumulating lipids, also their use as thesource of oil for biodiesel has been suggested.

These microorganism based oils are often called as single cell oils.Campbell 2008 and Strobel et al., 2008 have described optimization ofthe cultivation conditions of algae and fungi in different type ofbioreactors to maximize the yields of lipids and fatty acids forrefining of bio-fuels.

Alternative option to photosynthetic production of lipids is to utilizeheterotrophic organisms which produce lipids from organic molecules(such as sugars) without need for light. Single cell oil productionprocess using heterotrophic microorganisms comprises cultivatingmicroorganisms in aerated bioreactors, allowing cells to accumulatelipids, harvesting lipid-rich cells and recovering oil from cells(Ratledge et al., 2005, Meng et al., 2009).

Single-cell oils have traditionally been used as special products e.g.in health foods, not as commodity chemicals. In these kinds of singlecell oil production processes product volumes are relatively small andthe product is expensive. Therefore, the cost structure of theseprocesses allows the utilization of expensive feed raw materials andunit operations. Similar kind of production process has also beendescribed for the production of lipids for biodiesel production(Ratledge and Cohen 2008; Meng et al. 2009). However, as the product isan inexpensive commodity chemical, the process costs should not be onthe level of the process costs of special products. Further, the lipidyield by heterotrophic microorganisms is typically very low, less than20% weight percent of the fed sugar (Ratledge and Cohen, 2008).

Less expensive raw materials for use in lipid production byheterotrophic microorganisms have been suggested in some recent patentpublications. WO 2009/034217 A1 has described a fermentation method tomake paraffins, fatty acids and alcohols by waste materials andmicrobes. WO 2009/046375 A2 suggests the conversion of polysaccharidesderived from biomass into monosaccharides, or oligosaccharides andconverting them into biofuels by using recombinant microorganismscomprising exogenous genes that allow the microorganism to grow on thepolysaccharide as a sole source of carbon. US 2009/0064567 A1 disclosesthe production of biological oils by heterotrophic fermentation bygrowing microorganism of the kingdom Stramenophile by usingcellulose-containing feedstock as a main source of carbon. WO2009/011480A1 discloses the production of biological oils from depolymerisedcellulosic material by microalgae and fungi. US 2009/0148918 A1discloses a method of lipid manufacturing by culturing a microalgae onglycerol as a source of carbon. In addition WO 2009/009391 A2 disclosesthe production of fatty esters by first producing an alcohol compositionand providing it into a fatty ester production host. WO 2009/063138describes a method for treating organic material with water, acid oralkali and grinding. A precipitate and filtrate are separated and usedfor lipid production in a cultivation medium for a lipid producingmicroorganism.

Since the economy of the production of single cell oils for biofuels isof key importance, new cost-effective processes for lipid production forbiofuel production are still of growing interest.

SUMMARY OF THE INVENTION

One object of the present invention is to provide a cost-effectiveprocess for producing lipids for biofuel or for lubricant applications.

Another object of the present invention is to provide new microorganismswhich can be used in said process.

The invention described herein provides, in one aspect, a process forproducing lipids, in particular for biofuel or for lubricant use. Theinvention is based on the finding that Streptomyces bacteria are able toproduce effectively lipids on a medium comprising organic waste(s)and/or residue(s).

The process comprises cultivating bacterial cells of the genusStreptomyces in a medium comprising organic waste(s) or residue(s) ormixtures thereof as carbon and/or nutrient source(s). The processcomprises the recovery of lipids from the cells of the bacteria or fromthe cultivation medium. The lipids or a fraction thereof are useful asbiofuel and/or lubricant or as starting material for biofuel and/orlubricant production.

In various embodiments of the invention the cultivation medium cancomprise organic waste(s) or residue(s) from industry, includingagriculture, municipal waste or microbial residues.

Furthermore, the cultivation medium can comprise additional carbonsource(s), such as glycerol or a fraction from sugar or starch industry.

In one embodiment of the invention the process can use not sterilizedcultivation medium.

In another embodiment of the invention the process can use pasteurizedcultivation medium.

In some embodiments of the invention the cultivation medium can compriselipase inhibitors. Lipase inhibitors can be used to retard or hinder thehydrolysis of acylglycerols or degradation of lipids formed in theprocess.

In one embodiment of the invention the cultivation is carried out as abatch fermentation.

In another embodiment of the invention the cultivation is carried out asa fed-batch fermentation.

As disclosed herein the process produces lipids which comprise mainlyTAGs (triacylglycerols). Typically the amount of TAGs in the spentcultivation medium is at least 1 g/litre of the medium.

Various Streptomyces species can be used in the invention. The speciescomprise, preferably the species may be selected from the groupcomprising, more preferably the species may be selected from the groupof Streptomyces roseosporus, Streptomyces griseus, Streptomyces albus,Streptomyces peucetius, Streptomyces aureofaciens Streptomyces lividans,Streptomyces coelicolor, Streptomyces hygroscopicus, Streptomycesavermitilis, Streptomyces milbemycenius and Streptomyces lydicus.

Streptomyces strains comprise, preferably the strains may be selectedfrom the group comprising, more preferably the strains may be selectedfrom the group of strains Streptomyces roseosporus GAL4111, Streptomycesroseosporus G011, Streptomyces griseus GAL1005, Streptomyces albusGAL1001, Streptomyces peucetius D2, GAL4082, Streptomyces peucetius P55GAL4081, Streptomyces aureofaciens GAL1004, Streptomyces lividansGAL1002, Streptomyces coelicolor GAL1003, Streptomyces hygroscopicusGAL4051, Streptomyces avermitilis GAL1006, Streptomyces milbemyciniusGAL4211 and Streptomyces lydicus GAL1007.

Advantageous in the process of the present invention are Streptomycesspecies or strains that produce no or only low amounts of bioactivemetabolites.

In a specific embodiment of the invention Streptomyces species orstrains may be made deficient in producing bioactive metabolites.Examples of bioactive metabolites are for example antibiotic agents,such as lipopeptide antibiotics, for example daptomycin or milbemycin,or chemotherapeutic agents, such as daunomycin.

Strains producing low amounts of bioactive compounds or that are madedeficient in producing bioactive compounds are for example strainscomprising, preferably strains selected from the group comprising, morepreferably strains may be selected from the group of Streptomycesroseosporus GAL4111, Streptomyces roseosporus G011, Streptomyces griseusGAL1005, Streptomyces albus GAL1001, Streptomyces peucetius P55 GAL4081and Streptomyces peucetius D2 GAL4082 and Streptomyces milbemyciniusGAL4211.

In one aspect the invention provides a Streptomyces culture, whichcomprises

(a) a population of bacteria of the genus Streptomyces; and (b) acultivation medium comprising organic waste(s) or residue(s) or mixturesthereof as carbon and/or nutrient source(s).

In another aspect of the invention, the present invention provides newgenetically modified Streptomyces hosts capable of effective lipidproduction.

In one embodiment of the invention Streptomyces host cells may begenetically modified to express at least one gene of the lipidbiosynthesis pathway. In particular, the gene may be a gene encodingdiacylglycerol acyltransferase (DGAT) and/or a gene encoding3-ketoacyl-acyl carrier protein synthase III (FabH).

In one embodiment of the invention Streptomyces host cells may begenetically modified to express one or more of genes comprising,preferably selected from the group comprising, more preferably they maybe selected from the group of

-   (a) sco0958 (SEQ ID NO:1) and/or sco5888 (SEC) ID NO:2);-   (b) the closest homologue of said genes in a Streptomyces species;-   (c) a nucleotide sequence which hybridizes to at least one of said    genes or said homologues under stringent conditions;-   (d) a nucleotide sequence causing the same or an equivalent function    as gene products ID 101096381 or ID 101101330 have; and/or-   (e) a nucleotide sequence encoding an amino add sequence showing at    least 60% identity to SEQ ID NO: 3 or SEQ ID NO:4.

In particular, suitable genetically modified strains are strainscomprising, preferably selected from the group comprising, morepreferably strains selected from the group of G009, G010, G012, G013,G014, G015, G016, G017 and G019.

In one specific embodiment of the present invention provides newStreptomyces strains selected from the group of G009, G010, G013, andG017.

In one further aspect the present invention provides use of any of thehost cells, cultures or strains of Streptomyces for producing lipids andusing the lipids as biofuel and/or lubricant or as a starting materialfor biofuel and/or lubricant production.

In addition, in one aspect the invention provides products obtained byusing the process according to this disclosure.

Considerable advantages are obtained by means of the present invention.By means of the process and microorganisms presented here, it ispossible to produce effectively lipids for biofuel and/or lubricant, oras a starting material for biofuel and/or lubricant production. Theadvantages of the present invention can be summarized as follows:

In the present invention it has surprisingly been found thatstreptomycetes can produce high amounts of lipids when cultivated on amedium comprising organic waste(s) and/or residue(s). The use of organicwaste(s) and/or residue(s) as a carbon and/or nutrient source(s) reducesthe costs of the cultivation medium, in particular because waste(s)and/or residue(s) are in-expensive and need no or only littlepretreatment before use. The components of waste or residue materialsneed not to be necessarily separated, hydrolyzed (depolymerized),purified and/or sterilized before they are added to the cultivationmedium.

The yield of lipids produced by Streptomyces in the process can befurther increased by using lipase inhibitors in the cultivation medium.Lipase inhibitors are able to retard or hinder the hydrolysis ofacylglycerols or degradation of lipids formed in the process.

The process as described here produces lipids which comprise mainly TAGS(triacylglycerols). The preferred compounds suitable for chemicalprocessing for biofuel production are TAGs.

The efficiency of Streptomyces species or strains to produce lipids canbe further improved by making the species or strains deficient inproducing bioactive metabolites, such as antibiotic agents. The modifiedhost strain has more capacity to produce lipids, when it is notproducing bioactive metabolites.

The efficiency of lipid production can be further increased by producingnew genetically modified Streptomyces hosts which may be geneticallymodified to express at least one gene of the lipid biosynthesis pathway.

In the following, the invention will be examined more closely with theaid of a detailed description and with reference to some workingexamples.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 presents the process scheme.

FIG. 2 depicts the TLC (Thin Layer Chromatography) profile of the strainG009.

FIG. 3 shows the changes of PMV, cell mass, and dispersion of lipids insolid and liquid fractions in 5 day cultivation of the strain G009 inliquid TSB media. The growth cycle is about 36 hours after which celllysis takes place. The accumulation of TAGs takes place immediatelyafter the fast growth stage in 24 to 48 hours.

FIG. 4 presents an example of the accumulation of TAGs in differentmedia by G009. Samples from left to right are E05-14 medium after 0, 2,5 and 7 days, E05-15 medium after 0, 2, 5, and 7 day cultivation,standards COD (Cholesterol octadecanat), C (Cholesterol) and GTM(Glyceryl trimyristate), E05-16 medium after 0, 2, 5 and 7 day, E05-17medium after 0, 2, 5 and 7 day cultivation.

FIG. 5 presents an example of the accumulation of TAGs in differentmedia by the strains G017, G016, G013 and G011. Samples from left toright are GTM standard in concentrations of 40, 20, 10 and 5 g/l,samples of G017 after 0, 1, 2, and 5 day cultivation, samples of G016after 2, 3, and 6 days cultivation, samples of G013 after 1, 2, 5 and 6day cultivation, samples of G011 after 2, 3, and 6 day cultivation.

DETAILED DESCRIPTION OF THE INVENTION

“Biofuel” refers to solid, liquid or gaseous fuel mainly derived frombiomass or biowaste and is different from fossil fuels, which arederived from the organic remains of prehistoric microorganisms, plantsand animals.

According to EU directive 2003/30/EU “biodiesel” refers to amethyl-ester produced from vegetable oil or animal oil, of dieselquality to be used as biofuel. More broadly, biodiesel refers tolong-chain alkyl esters, such as methyl, ethyl or propylesters, fromvegetable oil or animal oil of diesel quality. Biodiesel can also beproduced from microorganism lipids, whereby microorganism lipid canoriginate from a bacterium, a fungus (a yeast or a mold), an algae oranother microorganism.

“Renewable diesel” refers to a fuel which is produced by a hydrogentreatment of lipids of an animal, vegetable or microorganism origin, ortheir mixtures, whereby microorganism lipid can originate from abacterium, a fungus (a yeast or a mold), an algae or anothermicroorganism. Renewable diesel can be produced also from waxes derivedfrom biomass by gasification and Fischer-Tropsch synthesis. Optionally,in addition to hydrogen treatment, isomerization or other processingsteps can be performed. Renewable diesel process can also be used toproduce jet fuel and/or gasoline. The production of renewable diesel hasbeen described in patent publications EP 1396531, EP1398364, EP 1741767and EP1741768.

Biodiesel or renewable diesel may be blended with mineral oil baseddiesel. Suitable additives, such as preservatives and antioxidants maybe added to the fuel product.

“Lubricant” refers to a substance, such as grease, lipid or oil, thatreduces friction when applied as a surface coating to moving parts. Twoother main functions of a lubricant are heat removal and to dissolveimpurities. Applications of lubricants include, but are not limited touses in internal combustion engines as engine oils, additives in fuels,in oil-driven devices such as pumps and hydraulic equipment, or indifferent types of bearings. Typically lubricants contain 75-100% baseoil and the rest is additives. Suitable additives are for exampledetergents, storage stabilizers, antioxidants, corrosion inhibitors,dehazers, demuisifiers, antifoaming agents, cosolvents, and lubricityadditives (see for example U.S. Pat. No. 7,691,792). Base oil forlubricant can originate from mineral oil, vegetable oil, animal oil orfrom a bacterium, fungi (a yeast or a mold), an algae or anothermicroorganism. Base oil can also originate from waxes derived frombiomass by gasification and Fischer-Tropsch synthesis. Viscosity indexis used to characterise base oil. Typically high viscosity index ispreferred.

The term “lipid” refers to a fatty substance, whose molecule generallycontains, as a part, an aliphatic hydrocarbon chain, which dissolves innonpolar organic solvents but is poorly soluble in water. Lipids are anessential group of large molecules in living cells. Lipids are, forexample, fats, oils, waxes, wax esters, sterols, terpenoids,isoprenoids, carotenoids, polyhydroxyalkanoates, nucleic acids, fattyacids, fatty alcohols, fatty acid esters, phospholipids, glycolipids,sphingolipids and acylglycerols.

The term “acyglycerol” refers to an ester of glycerol and fatty acids.Acylglycerols occur naturally as fats and fatty oils. Examples ofacylglycerols include triacylglycerols (TAGs, triglycerides),diacylglycerols (diglycerides) and monoacylglycerols (monoglycerides).

The present invention relates to methods for efficient production oflipids by streptomycetes using cultivation media comprising organicwaste(s) or residue(s) or mixtures thereof as a source of carbon and/ornutrient. In addition the cultivation media may comprise othercomponents, such as mineral salts typically used in cultivating saidmicroorganisms. The cultivation is carried out under conditions suitablefor lipid production. The cultivation is typically carried out in afermentor by using agitation and aeration.

In some embodiments of the invention organic waste(s) or residue(s) maybe used as the sole or main carbon and/or nutrient source, or in someembodiments as (a) supplement(s). The waste or residue may comprise oneor more different waste(s) or residue(s) or mixtures thereof.

If a waste or residue is the “main source of carbon and/or nutrient” inthe medium, it means that on the basis of weight, the amount of waste ishigher in the medium than the amount of pure ingredients (i.e. sugar) inthe medium.

If a waste or residue fraction is used “as a supplement” it means thaton the basis of weight, the amount of waste or residue fraction is lowerin the medium than the amount of pure ingredients (i.e. sugar) in themedium.

In the present invention it has surprisingly been found thatStreptomyces bacteria accumulate high amounts lipids and in particularof the triacylglycerols (TAGs) when cultivated on waste and/or residuematerials.

Bacteria of the genus Streptomyces are well known in pharmaceuticalindustry. It is known that streptomycetes produce small molecules,useful enzymes and a variety of other metabolites by primary andsecondary metabolism. Typically, aerobic fermentation processes aresuitable to a variety of Streptomyces species since the methodology hasbeen developed in many circumstances using these bacteria as modelorganisms. In the prior art processes streptomycetes are typicallycultivated in complex media to enhance the accumulation of industriallyuseful metabolites, such as antibiotics. The costs of these fermentationprocesses are heavily influenced by material and purification costs.Sterilization needed to maintain the fermentation free of contaminantsis extremely energy-consuming and the sterilization costs are high. Alsowhen producing bulk antibiotics the energy needed for sterilization ofthe medium forms the major cost category in the process, although theyare manufactured in large and simple fermentation tanks.

In the present invention it has surprisingly been found thatstreptomycetes can produce high amounts of lipids when cultivated onwaste and residue materials. It is remarkable that the components ofwaste or residue materials need not to be necessarily separated,hydrolyzed (depolymerized), purified and/or sterilized before they areadded to the cultivation media. Hence, in some embodiments wastematerial can be added to cultivation medium without any separation,hydrolysis (mechanical, chemical, or enzymatic), purification orsterilization. E.g. lignocellulosic materials can be used in cultivationand lipid production without hydrolysis (depolymerization) ofpolysaccharides. In other embodiments it can be added in crude form,i.e. comprising some preliminary purification, but being not purified toseparate components. Furthermore, waste or residue can be added as such,or depending on the structure of the material, it can be added ingrounded or mashed form to the cultivation medium. Wastes and/orresidues can also be utilized in partly or completely purified,separated and hydrolyzed (depolymerized) form for lipid production byStreptomyces.

In the present disclosure “organic waste or residue” refers inparticular to waste material, of which the components are not, or atleast not completely, separated, hydrolysed (depolymerised) and/orpurified. The use of waste or residue material without separation,hydrolysation (depolymerization) and/or purification of the componentsmakes the process of the present invention more cost-effective comparedto the use of pure ingredients. Nevertheless, in some embodiments of theinvention pure ingredients may be used in cultivation media as carbonsources in addition to the waste material(s).

“Non-sterile organic waste or residue or cultivation medium comprisingorganic waste or residue” refers in particular to waste or residuematerial or medium, which is not sterilized. In some embodiments, thewaste material or medium may be pasteurized.

By sterilization it is typically meant that the waste or residuematerial or medium comprising the waste or residue material is treatedwith high temperature, usually at 121° C., or higher, for at least 15minutes, or for at least 20 minutes.

“Pasteurization” refers to the heating of a waste or residue material ormedium comprising waste or residue material at 60° C.-75° C. for 2-30minutes. As described herein even with high content waste or residuefractions up to 200 g/l, no living cells or spores were detected at ISA(Tryptone Soy Agar). In cultivations where pasteurized media instead ofsterilized media were used, no differences were found in the growth ofstreptomycetes. The cultivation medium can comprise organic waste(s) orresidue(s) or their combination with pure nutrients.

In some embodiments of the present invention a cultivation mediumcomprising organic waste or residue can be used as such, in someembodiments without sterilization by any method, or withoutpasteurization. “Non-sterile” means in those embodiments thatcultivation medium with waste or residue material is not sterilized byany method.

In the present disclosure the waste or residue material or mediumcomprising the waste or residue material is not sterilized, inparticular it is not sterilized with high temperature, such as at 121°C., or higher, or it is pasteurized.

In the present disclosure “organic waste or residue” refer in particularto waste or residue from industry including agriculture, municipal wasteor microbial residue. Such waste or residue is typically (i) not used asfood for people or animals and (ii) is formed in large quantities(typically in thousands or in millions of tonnes per annum globally). Alarge group of organic wastes from industry fulfils these criteria.“Organic waste or residue” refers to any waste or residue material orfraction that is biologically degradable.

Industrial waste or residue can comprise offal residue, organic waste orresidue from food or feed production, e.g. from bakery, brewery, e.g.mash, malt extract, slaughter house, e.g. offal residue, meat or fishdebris, sugar industry e.g. sugar beet pulp, or wood derived cellulosicor lignocellulosic materials or residues, or agricultural residues, suchas grain residues, for example bran, chaff, straw, stalks, sugar canebagasse, or other plants such as cellulosic crops, switchgrass, reedcanary grass, Miscanthus, fiber sorghum, fiber cane, or plant residues,such as corn steep liquor (CSL), or glycerol for example from biodieselproduction.

Municipal waste can comprise municipal sludge, waste paper, biowaste ofinstitutional kitchen or households, organic waste of garden or organicwaste of food production.

Microbial waste can comprise microbial cells or cell debris (for examplelactobacilli, streptomycetes) for example from industrial processesbased on the use of microorganisms, or algae debris (e.g. Phaeodactylum,Chlorella, Dunaliella, Nannochloropsis).

Preferred waste(s) or residue(s) are lignocellulosic wastes or residuesfrom agriculture and wastes or residues from pulp and paper industryprocesses including cellulosic (energy) crops.

Preferred waste(s) or residue(s) are also biowaste from institutionalkitchen or from food or feed industry.

Preferred waste(s) or residue(s) are also microbial wastes or residues,in particular algae or bacterial waste or residues. Organic waste orresidue material refers in particular to any organic waste or residue,which Streptomyces can use for growth and/or for lipid production.

In some embodiments of the invention organic wastes or residues can besupplemented with an additional carbon source, such as glycerol, afraction from sugar or starch industry, sugar or starch syrup(s) orpurified sugar(s) or any mixtures thereof. More specifically organicwastes or residues can be supplemented with crude products from sugarand starch industry, such as sugar syrups, starch syrups, glucose(dextrose) syrups or molasses. Further, the wastes can be supplementedwith single or mixes of purified C6 or C5 sugar(s) such as glucose,fructose, mannose, xylose or arabinose, sugars dimers such as sucrose orlactose or sugar polymers such as cellulose, starch or xylan. The use ofsupplements from sugar or starch industry or other purified sugars mayincrease and accelerate the growth of streptomycetes and/or lipidaccumulation.

The term organic waste or residue encompasses also the term “waste orresidue fraction”. The term “waste or residue fraction” refers, forexample, to waste produced as a side (branch) product or side (branch)product from an industrial process producing some other product as themain product.

Within the scope of the present invention is the use of organic wastesor residues alone or in any combination or mixture.

In terms of lipid accumulation in the cultivations it is advantageous touse waste or residue to starch syrup or sugar syrup in the ratio from10/1 to 1/2, preferably from 5/1 to 1/1. For example, good accumulationof lipids was found in cultivations containing 10-50 g/l of waste with10 g/l of sugar syrup.

Furthermore, as described herein, it is beneficial for cell growth tosupplement industrial organic waste or residue material with microbialresidues, such as cell debris. As herein described good growth was foundfor example in cultivations where cell debris, in particular frombacterial or algal origin was used together with organic waste material,such as CSL (Corn Steep Liquor), and/or with Farmamedia as mediumsupplement. For example, bacterial debris from streptomycetes orlactobacilli and/or algae debris from Phaeodactylum, Chlorella,Dunaliella and Nannochloropsis can be used in the invention. Anotherbeneficial supplement to cell growth according to this invention issoya.

Starch is advantageous to accumulation of lipids. However, economicallyit is of benefit, if starch is replaced by agricultural residues, suchas bagasse, bran, chaff or straw. Algae or microbial cells or residues,such as bacterial or algae debris, biowaste, meat, CSL, OVR (grain(barley) protein feed), mink feed, and/or offal can replace the proteinbased ingredients typically useful in streptomycetes fermentation, suchas yeast extract, Farmamedia, and/or soya.

In the cultivation media waste or residue in a wide scale can be used.In some embodiments the amount of waste or residue in the cultivationmedia can vary from 1 g/l to 400 g/l, typically from 2 g/l up to 200g/l, in some embodiments from 20 to 150 g/l, in some other embodimentsfrom 50 to 100 g/l. Streptomycetes have been found to use wastefractions effectively for growth and the accumulation of lipids has beenfound to be similar when compared to cultivations with pure nutrients.

As described herein the microbial cell growth may be followed by usingPackage Mycelia Volume (PMV), cell mass changes, plating, microscopy andvisual analyses.

High density cell growth is obtained with several waste fractions. Invarious embodiments it varies from 1 to 200 g/l, typically from 10 to130 g/l as dry cell mass.

The PMV values with several waste fractions varies from 1% to 80%,typically from 6% to 40% in the standard cultivation conditions (28° C.,150 rpm).

It is, however, clear that even higher cell densities can be obtained byadjusting the fermentation conditions accordingly. On the other handcell mass does not directly correlate with the amounts of lipidsaccumulated.

Within the scope of the present invention is also the use of wastematerial in combination with pure ingredients.

Hydrolysed or partially hydrolyzed (depolymerised) organic waste(s) orresidue(s) are useable in the present invention. Wastes or residues canbe hydrolysed by (thermo)mechanical, chemical or enzymatic hydrolysis.For example, waste or residue material can be treated by suitableenzymes to digest crude ingredients. Suitable enzymes are for examplecellulases, hemicellulases, xylanases and pectinases. Alsostreptomycetes possessing both digestive enzyme functions and havingcapability to accumulate lipids can be used in the invention. Hence,preprocessing of the waste is not necessary. For example suitablestrains for this purpose are those belonging to S. roseosporus and Salbus species.

Within the scope of the present invention are, batch, fed-batch andcontinuous cultivations.

In cultivations with solid or semisolid substances as raw materials(carbon and/or nutrient sources), biomass may decrease in the first daysof cultivation due to the utilization of raw materials by microorganismsincreasing in the following days.

In some embodiments of the invention Streptomyces produce lipids asestimated by dry mass of chloroform extracts derived from thecultivations at least 0.1 g/litre, preferably at least 0.5 g/litre, morepreferably at least 1 g/litre, still more preferably at least 5 g/litreof the spent cultivation medium, in some embodiments at least 10g/litre, typically 5-30 g/litre, in some other embodiments 10 to 25g/litre up to 150 g/litre estimated as dry mass of chloroform extracts.It varies in some embodiments in the range of 1-200 g/litre, beingtypically 5-100 g/litre of spent cultivation medium.

In some embodiments of the invention the concentration (titre) of TAGsis generally at least 0.1 g/l (0.1 kg/1000 litre), preferably at least0.5 g/l (0.5 kg/1000 litre), more preferably at least 1 g/litre (1kg/1000 litre), still more preferably at least 5 g/litre (5 kg/1000litre) of spent cultivation medium. It usually varies from 0.5 to 150kg/1000 litre, in some embodiments 1 to 100 kg/1000 litre, in some otherembodiments 1 to 70 kg/1000 litre, being typically about 5-50 kg/1000litre, in some embodiments 10 to 30 kg/1000 litre, in some otherembodiments 15 to 25/kg/1000 litre of spent cultivation medium.

The improvement of TAG production by the genetically modified strains isgenerally at least 10%, typically at least 30%, in some embodiments atleast 50% and even 100-300% compared to the parent strains.

“Spent cultivation medium” refers to a medium used in the cultivation ofmicroorganisms and comprising the products accumulated by themicroorganisms. Spent cultivation medium comprises solid phase such asbiomass, like microorganisms and solid raw materials, as well as liquidphase. Therefore, spent cultivation medium comprises productsaccumulated inside the microorganism cells and released from the cellsto the medium. The spent cultivation (or culture) medium can be calledalso spent cultivation broth. “Cultivation medium” refers usually tocultivation medium before use (before inoculation and cultivation).

Furthermore, in various embodiments of the invention the amount of totallipids is at least 10% by its weight of dry cell mass, typically it is20-60% by its weight of dry cell mass.

In various embodiments of the invention the lipid fraction produced bystreptomycetes comprises mainly of TAGs. This means that at least 30wt-%, in some embodiments at least 50 wt-%, in some other embodiments atleast 80 wt-%, yet in some further embodiments at least 70 wt-%, yet insome further embodiments at least 80 wt-%, or yet in some furtherembodiments at least 90 wt-% of the lipid fraction is TAGs.

The lipid profile characteristic to a non-modified (parent strain) orgenetically modified strain cultivated on pure sugar comprises typicallyabout 70 to 95 wt-% of TAGs and about 5 to 30 wt-% of oligomers,diacylglycerols and monocylglycerols and free fatty acids. The fattyacids of non-modified or genetically modified Streptomyces strainscomprises typically of branched and straight chain fatty acids. Thefraction of branched fatty acids can be between 20 to 80 wt-%, andtypically is between 40 to 70 wt-%. The content of methyl-branched fattyacids can be between 45 to 50%. The majority of fatty acids determinedwere saturated.

Further, Streptomyces lipids also contain squalene or squalene derivatestypically 2 to 5 wt-%, which can be used as base oils or startingmaterial for base oils for lubricant applications.

Lipid profiles of Streptomycetes have been reported in literature byOlukoshi and Packter (1994), by Packter and Olukoshi (1995).

The composition of the lipid profile most likely changes whenStreptomyces is cultivated on a medium comprising waste(s) orresidues(s) instead of pure sugar, because lipid extraction may compriselipids from the waste (for example membrane phospholipids areextracted).

“Lipids” generally refer here to the lipids produced by Streptomycesduring the cultivation and to the lipids contained in the components ofthe culture medium, in particular waste or residue material in theculture medium. “A lipid fraction” refers to a fraction of the lipids,such as TAGs or branched fatty acids or squalenes.

In some embodiments of the invention, cell debris and even algaeresidues give remarkable quantities of lipids dominating by TAGs. Thepreferred nutrient and/or C-source of algae are Chlorella andDunaliella, which gave the highest quantity of TAGs in the spentcultivation medium.

As described herein, prolonged batch cultivations of the Streptomycesstrains in waste fractions (typically exceeding 7 days) and in pureingredients based medium (typically exceeding 5 days) result indisappearance of TAGs and some other lipids, suggesting that lipids aredegraded.

In some embodiments of the invention lipase inhibitors may be added tothe culture medium. Suitable lipase inhibitors are for example silverions (Lee & Lee, 2006) or cationic substances (Cote and Sharech, 2008).By using lipase inhibitors it is possible to inhibit degradation oflipids and enhance the accumulation of TAGs. Even small concentration ofinhibitors, for example AgNO₃ in concentration 0.04 to 0.06 g/l, areuseful as is shown in Example 12.

In some embodiments of the invention the inoculation of the cultivationmedium is carried out by streptomycetes mycelia or spores. In preferredembodiments the inoculation is carried out by using spores. The amountof spores can be 10⁷-10⁹ spores/one litre (e.g. 5×10¹² spores/500litre).

In some embodiments of the invention the cultivation can be carried outin 1 to 21 days, typically in 2 to 14 days, preferably in 2 to 6 days.In some embodiments lipase inhibitors may be added in the middle (orafter the start or before the end) of the cultivation.

In various embodiments of the invention the cultivation temperature isusually 20 to 36° C., typically it is 26-30° C.

The cultivation of streptomycetes for lipid production is typicallycarried out in various embodiments of the invention in a liquid culturemedium in a fermentor preferably under suitable aeration and agitation.The mixing speed varies typically from 0 to 800 rpm, being typically150-600 rpm.

As wastes or residues may contain lipids it is rational to follow up theuse of the external lipids to determine the lipids formed by thebacterial strains. As described herein the utilization of externallipids was followed up by changes in solid mass and changes in lipidprofiles. It was shown that the biomass decreased up to 36-48 hours fromthe beginning of the cultivation and started to increase after that. Thecycle time is dependent on the degree of processing of waste in use.Nevertheless, no remarkable differences were found after five days ofcultivation when cultivation was followed up to 8 days. The lipids weredetectable in supernatant in the 0 sample and increased in a solidfraction up to 4-5 days. After that the lipids reduced in the cellfraction, and a part of the lipids were found in supernatant andprobably a part of the accumulated lipids were used for metabolism. FIG.3 demonstrates the follow up of PMV, cell mass and lipids of solid andliquid fractions in 8-day cultivation, It can be concluded that lipidsdetected after 3 days were derived from bacterial metabolism.

The lipid yields (g_(lipids)/g_(glucose)) determined to fed sugar variedin the range of 10-55%. The yields were determined based on the fed puresugar and did not consider the sugar included in wastes and residues.Theoretical maximum of lipid yield from glucose is 33%. However inpractice, the maximum lipid yield is 20-22% (Ratledge and Cohen 2008).Thus, lipid yields higher than 22% indicate that lipids were generated(produced) from waste and residue materials.

Streptomyces Strains

By Streptomyces bacteria are here meant any species or strains belongingto the genus Streptomyces.

Preferred species in various embodiments of the invention are speciescomprising, preferably are selected from the group comprising, morepreferably are selected from the group of Streptomyces roseosporus,Streptomyces griseus, Streptomyces albus, Streptomyces peucetius,Streptomyces aureofaciens Streptomyces lividans, Streptomycescoelicolor, Streptomyces hygroscopicus, Streptomyces avermitilis, andStreptomyces lydicus. Most preferred species are selected from the groupof Streptomyces roseosporus, Streptomyces griseus, Streptomyces albus,Streptomyces peucetius, Streptomyces milbemycinius and Streptomycesaureofaciens.

More specifically, the Streptomyces strain comprises, may be selectedfrom the group comprising, more preferably is selected from the group ofStreptomyces roseosporus GAL4111, Streptomyces roseosporus G011,Streptomyces griseus GAL1005, Streptomyces albus GAL1001, Streptomycespeucetius D2 GAL4082, Streptomyces peucetius P55 GAL4081, Streptomycesaureofaciens GAL1004, Streptomyces lividans GAL1002, Streptomycescoelicolor GAL1003, Streptomyces hygroscopicus GAL4051, Streptomycesavermitilis GAL1006, Streptomyces lydicus GAL 1007. Most preferably thestrain is selected from the group of Streptomyces roseosporus GAL4111,Streptomyces griseus GAL1005, Streptomyces albus GAL1001, Streptomycespeucetius D2 GAL4082, Streptomyces milbemycinius GAL4211 andStreptomyces aureofaciens GAL1004

It is known that various streptomycetes species can accumulatetriacylglycerols (TAGS) in small quantities: S. albus (Alvarez andSteinbüchel, 2002); S. lividans (Packter N D Olukoshi, 1995, Alvarez andSteinbüchel, 2002); S. coelicolor (Arabolaza al., 2008, Alvarez andSteinbüchel, 2002); S. hygroscopicus (Gesheva et al., 1997); S.aureofaciens (Bëhel and Jilek, 1969); S. griseus (Suutari et al., 1992,Alvarez and Steinbüchel, 2002); S. avermitilis (Kaddor et al., 2009;Novak et al. 1992); and S. lydicus (Nagao et al., 1991). The publicationby Wälternann et al. (2006) characterizes gene products involved in thebiosynthesis of neutral lipids in bacteria. However, the production oflipids by using a typical prior art fermentation process is relativelyenergy-consuming and thus expensive.

In this disclosure Streptomyces bacteria refer in particular to purecultures of bacteria belonging to genus Streptomyces. In someembodiments different Streptomyces species or strains in combination canbe cultivated subsequently or together. Furthermore, in this disclosureStreptomyces bacteria refer in particular to Streptomyces species andstrains capable of naturally producing lipids. In some embodiments ofthe invention the capability of Streptomyces species or strains can beimproved by introducing nucleic acid sequences responsible for lipidproduction into Streptomyces strains and expressing these nucleic acidsequences under regulatory elements, such as a promoter, recognized bythe Streptomyces host.

It is also possible to improve the Streptomyces species or strains usedin lipid production by making the host strains deficient in producingendogenous bioactive products, such as lipopeptide antibiotics. This canbe carried out by molecular biology methods well known in the art.Useful methods are for example deletion of the gene(s) responsible ofproducing bioactive product(s) or various mutagenization methods, suchas site-directed mutagenesis.

“Making deficient of a gene” refers either to a genetic modification ofthe Streptomyces host to delete or truncate a specific gene or a geneticmodification of the Streptomyces host resulting in reduced expression ofthe gene or reduced activity of the gene product by any suitable method.By “inactivation” is meant a genetic modification (usually deletion)resulting in complete loss of activity of a gene product.

From Streptomyces strains can be generated mutants not producing desiredbioactive products, such as antibiotics. Mutants can be generated forexample by random methods using a chemical mutagen, such as NTG,(N-methyl-N′-nitro-N-nitrosoguanidine). Colonies that fail to produceantibiotics can be tested by a suitable assay, such as antibacterialassay. Furthermore, the accumulation of lipids can be analysed forexample by HPLC. From Streptomyces strains can be generated mutants notproducing desired bioactive products, such as antibiotics also bytargeted inactivation of certain genes, such as inactivation of thefirst biosynthetic gene(s) of the bioactive product. This wasexemplified by inactivating the polyketide biosynthesis (PKS) genes in aStreptomyces host. The gene product was truncated by a biomarker. Theclones obtained were studied for expression of antibacterial propertiesand analyzed for production of milbemycins by HPLC.

In the present invention it was surprisingly found that Streptomycesstrains can produce significant amounts of lipids without geneticengineering of their lipid synthesis pathway. However, as discussedabove, it may be of advantage that the host is made deficient ofproducing bioactive products, such as lipopeptide antibiotics.

In the present invention it was surprisingly found that Streptomycesmilbemycinius species was capable of producing high amount of lipids.High lipid production was exemplified in particular with a S.milbemycinius strain made deficient of producing antibiotic milbemycins.As is described in the examples a S. milbemycinius strain was able toproduce lipids 20 g/l or more. The efficiency of conversion of pureglucose or glucose derived from starch was 33%. The amount of TAGs wasin the range of 80-90% of all lipids.

In the context of the work resulting in the present invention, the lipidproduction of Streptomyces strains from various Streptomyces species andstrains was studied. In some Streptomyces species and strains the lipidsynthesis pathway was genetically modified. These experiments werefollowed by experiments where the strains were cultivated on media,where waste or residue materials were used as carbon and/or nutrientsource. The production of lipids by the strains of Streptomyces genuswas exemplified by using 11 Streptomyces strains. The strains werestudied for accumulation of metabolites including lipid fraction,triacyiglycerides referred to as TAGs herein. All tested strainsaccumulated detectable quantities of TAGs and surprisingly, four out ofthe 11 tested Streptomyces strains were very fast growing giving wetcell mass exceeding 200 g/l in two to three days (see Table 1). Thesestrains were from species Streptomyces aureofaciens, Streptomycesroseosporus, Streptomyces griseus and Streptomyces albus. The strainswere Streptomyces aureofaciens GAL1004, Streptomyces roseosporus GAL4111and the mutant derived from it, G011, Streptomyces griseus GAL1005 andStreptomyces albus GAL1001. The strains were further cultivated andanalyzed for TAG production. Also, the ability of the strains to retaintheir non-producing character of bioactive metabolites during storagewas verified.

As described herein 11 Streptomyces strains were cultivated in typicalcultivation conditions to enhance the growth and also accumulation ofsecondary metabolites. The media used were TSB, 2*TY and E05. Thecultivation conditions in a shaker were, 28° C., 30° C., and 34° C. withagitation of 150 and 300 rpm.

The content of the cultivation media were:

TSB: 17 g/l pancreatic digest of casein, 3 g/l enzymatic digest ofsoybean meal, 2.5 g/l dextrose, 5 g/l sodium chloride, 2.5 g/ldipotassium phosphate;2*TY: 16 g/l of tryptone pepton, 10 g/l yeast extract, 5 g/l NaCl;E05: 20 g/l of dextrose, 20 g/l of starch, 5 g/l of farmamedia, 2.5 g/lof yeast extract, 1 g/l of MgSO₄.7H₂O, 1 g/l of KH₂PO₄, 3 g/l of CaCO₃,3 g/l of NaCl.

Table 1 shows characters of the strains and the relevant results ofcultivations done in TSB media. The TAGs were estimated by TLC platecompared to standard.

TABLE 1 Growth time In The Galilaeus' days (from highest Cell mass TAGscode Strain Characters growth curve) PMV wet/dry g/l (g/l) GAL1001 S.albus Fast growth cycle 2 10 275/42 0.5 and easy to cultivate.Non-producer of bioactive metabolites. GAL1002 S. lividans Fast growthcycle. 3  8 102/13 0.1 GAL1003 S. coelicolor Fast growth cycle. 2 10127/14 0.1 Well-known strain. 3 days GAL4051 S. hygroscopicus Fastgrowth cycle. 2 10 125/13 0.1 3 days GAL1004 S. aureofaciens Fast growthcycle. 2 16 220/46 0.5 2 and 3 days GAL1005 S. griseus Fast growthcycle. 2-3 12 206/47 0.5 Produces bioactive 3 days compounds ofdifferent chemical classes. Well- known strain. GAL4111 S. roseosporusFast growth cycle 1 10 280/40 0.5 and easy to cultivate. Produces cycliclipopeptide where peptide synthesis could be inactivated. GAL1006 S.avermitilis Fast growth cycle. 2-3 16 210/19 0.1 GAL1007 S. lydicus Fastgrowth cycle. 2 10 112/15 0.1 GAL4081 S. peucetius Inactivated in 5  6114/8 0.1 P55 production of secondary metabolites (anthracycline)GAL4082 S. peucetius D2 Inactivated in 2 10 140/18 0.5 production ofsecondary metabolites (anthracycline)

The strains that are able to grow well determined by wet cell massand/or as PMV-value, and to accumulate detectable levels of lipids in ashort cultivation time, are preferable strains for further developmentconcerning strain improvement for lipids accumulation and fordevelopment of fermentation conditions.

Genetically Engineered Strains for Enhanced Oil Production

The construction of recombinant hosts (i.e. genetically manipulatedstrains GMO) producing efficiently lipids was exemplified herein byintroducing genes involved in the biosynthesis of lipids into someStreptomyces hosts having the capability of effectively accumulatinglipids naturally.

Both the original strains and the clones carrying the genes involved inlipid biosynthesis were cultivated in a large variety of waste andresidue materials including biowaste. Unexpectedly, the strains wereable to grow and produce lipid fraction on waste or residue fractionswith and even without additional carbon source.

Cultivations revealed a fast growth cycle time: the stationary phase wasreached in 24 hours or even before while accumulation of lipidscontinued even up to 6 days thereafter. The dry/wet cell mass incultivation was not remarkably increased by the clones compared to theparental strain. However, remarkable increase in lipid accumulation,even up to 300% improvement compared to the parent strains was observed,in particular in the main fraction TAGs.

As described herein streptomycetes hosts showing suitable properties forindustrial useful bio-fuel fermentation processes can be furtherimproved by any known strain improvement methods, such as naturalselection, random mutagenization, and by genetic engineering.

Suitable genes to improve the accumulation of lipids comprise variousgenes encoding enzymes involved in fatty acid biosynthesis. Suitablegenes are in particular gene encoding diacylglycerol acyltransferase(DGAT) (EC 2.3.1.20) and gene encoding 3-ketoacyl-acyl carrier proteinsynthase III (FabH) (EC 2.3.1.41).

A gene encoding DGAT function (EC 2.3.1.20) is, for example, sco0958(SEQ ID NO:1), and a gene encoding 3-ketoacyl-acyl carrier proteinsynthase III (FabH) (EC: 2.3.1.41) is, for example, sco5888 (SEQ IDNO:2). The gene sco0958 (ID101096381) catalyzes the ultimate step in thebiosynthesis of TAGs (Arabolaza et al., 2008) and sco5888 (ID101101330)(Li et al., 2005) is responsible for the first elongation step in thebiosynthesis of fatty acids. The genes sco5888 and sco0958 originatefrom S. coelicolor.

Within the scope of the invention are also the closest homologues ofsaid genes sco0958 and sco5888 in various Streptomyces species.

Within the scope of protection are also nucleotide sequences whichhybridize to at least one of said genes or said homologues understringent conditions.

Within the scope of invention are also nucleotide sequences causing thesame or an equivalent function as gene products ID 101096381 or ID101101330.

Within the scope of the present invention are also a nucleotide sequenceencoding an amino acid sequence showing at least 60% identity,preferably at least 65%, preferably at least 70%, preferably at least75%, preferably at least 80%, preferably at least 85%, more preferablyat least 90%, still more preferably at least 95%, more and morepreferably at least 98% identity to amino acid sequences SEQ ID NO:3 orSEQ ID NO:4.

Within the scope of the present invention are nucleotide sequencescausing the same function or equivalent function as said genes sco0958(ID101096381) and sco5888 (ID 101101330). Such nucleotide sequences maybe fragments or derivatives of said genes, the closest homologues ofsaid genes in other Streptomyces species or nucleotide sequences whichhybridize to at least one of said genes or said homologues.

The hybridization is preferably carried out under stringenthybridization conditions. Stringent conditions can be defined ashybridization at 65° C. in a low salt concentration, 1.5 mM sodiumcitrate, pH 7.0 and 0.015 NaCl, according to Boehringer Mannheim'smanual, DIG System User's Guide for Filter hybridization.

It is evident that small variations in the nucleotide sequence of a genedo not significantly change the catalytic properties of the encodedprotein. For example many changes in the nucleotide sequence do notchange the amino acid sequence of the encoded protein. Also an aminoacid sequence may have variations, which do not change the functionalproperties of a protein, in particular they do not prevent an enzymefrom carrying out its catalytic function. Such variations in thenucleotide sequence or DNA molecules or in an amino acid sequence areknown as “functional equivalents”, because they do not significantlychange the function of the gene to encode a protein with a particularfunction, e.g. catalyzing a particular reaction or, respectively, changethe particular function of the protein. Within the scope of the presentinvention are functional equivalents, including fragments orderivatives, or closest homologues of the nucleotide sequence SEQ IDNO:1 or SEQ ID NO:2, or of the amino acid sequences SEQ ID NO 3 or SEQID NO:4, respectively.

Streptomyces capable of producing enzymes involved in lipid biosynthesiscan be screened, the activity on various substrates can be determined,and the enzyme characterized. Nucleotide sequences encoding enzymesinvolved in lipid biosynthesis in various organisms can be isolated andthe amino acid sequences can be compared with the amino acid sequencesSEQ ID NO: 3 and SEQ ID NO:4. A person skilled in the art can alsoidentify a conserved region in the nucleotide or amino acid sequence andclone a gene fragment using PCR techniques. After sequencing thefragment the complete gene can be obtained for example by using cDNAlibrary in a vector. A nucleotide sequence encoding the enzyme can beidentified also by nucleic acid hybridization.

Standard molecular biology methods can be used in the cloning of thegenes i.e. in the isolation and enzyme treatments of DNA, in E. colitransformations, the isolation of a fragment comprising the gene byamplification in a PCR reaction (Coen D M, 2001) and in the techniquesfor codon change. The basic methods used are described in the standardmolecular biology handbooks, e.g. Sambrook et al. (1989) and Sambrookand Russell (2001). Insertion of the nucleotide sequence under a strongpromoter in an expression vector, transfer of the vector into suitablehost cells and cultivation of the host cells in conditions provokingproduction of said enzyme. Methods for protein production by recombinanttechnology in different host systems are well known in the art(Gellissen, 2005).

Genetically modifying a Streptomyces host to express an endogenous orexogenous gene can be carried out for example by introducing into aStreptomyces host an exogenous gene from another Streptomyces species oran additional copy or copies of an endogenous gene. The gene may beexpressed under a promoter recognized by the Streptomyces host. In someembodiments the gene may be expressed under another promoter resultingin increased expression of the gene. Alternatively the Streptomyces hostmay be genetically modified so that either the gene is more abundantlyexpressed or that the activity of the gene product is increased.

The term “endogenous gene” refers here to a gene which is natural to theStreptomyces host.

The term “exogenous gene” refers here to a gene which is not natural tothe Streptomyces host.

The “closest homologue of an S. coelicolor gene”, in other Streptomycesspecies refers here to a gene with the highest percentage of identicalnucleotides in sequence alignment of the S. coelicolor gene and thegenes of the other species; or a gene whose protein product has thehighest percentage of identical amino acids to the protein productencoded by the S. coelicolor gene. By “closest homologue” is meant inparticular a gene or nucleotide sequence having at least 60%, preferablyat least 65%, preferably at least 70%, preferably at least 75%,preferably at least 80%, preferably at least 85%, more preferably atleast 90%, still more preferably at least 95%, more and more preferablyat least 98% nucleotide or amino acid sequence identity compared to aspecific S. coelicolor gene (SEQ ID NO:1 or SEQ ID NO:2) or product ofsaid gene (SEQ ID NO:3 or SEQ ID NO:4).

The term “identity” refers to the identity between two nucleic acid oramino acid sequences, respectively compared to each other from the firstnucleic acid to the last nucleic acid or from the first amino acidencoded by the corresponding gene to the last amino acid. The identityof the full-length sequences can be measured by using Needleman-Wunschglobal alignment program at EMBOSS program package (European MolecularBiology Open Software Suite; Rice et al., 2000) The program version canbe 2.9.0 and the parameters: EMBLOSUM62, Gap penalty 10.0, Extendpenalty 0.5.

“Genetical modification” of a Streptomyces host means here any geneticmodification method by which a Streptomyces host is modified to expressa specific endogenous or exogenous gene and/for to be deficient of aspecific gene or genes.

Genetical modification methods for a Streptomyces host are available andwell known for a person skilled in the art and disclosed for example inKieser et al, 2000.

As described herein a suitable method for introducing a gene into aStreptomyces host is for example protoplast transformation.

The vectors for introduction of the gene sequences, typically forexample PCR fragments, into the host strains may be selected among anyvectors that are able to introduce the cloned fragment into the hoststrain. Integration vectors, medium copy number and high and low copynumber vectors to introduce the fragments into suitable hosts can besuccessfully used.

Suitable vectors for transferring of the nucleic acid fragments intoStreptomyces hosts are for example pIJE486 (Ylihonko et al., 1996) andpHJL401 (Kieser et al., 2000).

The most preferred host strains are streptomycetes strains shown inTable 1, in particular the strains GAL1001 and GAL4111 or any mutantstrains derived from said strains.

Nevertheless, it is advantageous to use mutant strains unable toaccumulate bioactive compounds in culture broth for commercialproduction of bio-fuels. For this purpose the most preferred strains areGAL1001 and G011.

As described herein S. roseosporus GAL4111 and a derivative thereofdeficient in producing endogenous bioactive products, S. roseosporusG011, and GAL1001 were genetically modified by using genes involved inthe biosynthesis of lipids.

There are several genes involved in lipid metabolism in bacteria. In thepresent disclosure it has been shown that the genes sco0958 and sco5888either separately or in combination surprisingly increased thequantities of TAGs accumulated by streptomycetes. sco0958 is responsiblefor the terminal reaction in triacylglyceride (TAG) biosynthesis beingan esterification of diacylglycerol (DAG) of a fatty acid molecule(Arabolaza at al., 2008). sco5888 is 3-ketoacyl acyl carrier proteinencoding the first elongation step of fatty acid biosynthesis (Li at,2005). The genes may be cloned using any suitable cloning method.According to one embodiment of the invention the cloning is carried outby PCR from the chromosomal DNA using homologous primers.

The genes were introduced into the said strains by protoplasttransformation. The strains carrying these genes separately or incombination showed increased accumulation of TAGS.

The GMO strains selected and designated as G009, G010, G013, G014, G015,G012, G016, G017, and G019 carry an intact plasmid retaining cultivationproperties and lipids accumulation after several passages.

The best strains for accumulation of lipid fractions enriched in TAGswere the clones derived from GAL1001, designated as G009, G013 and G017.

As described herein the vectors pIJE486 (Ylihonko et al., 1996) andpHJL401 (Kieser et al., 2000) were used to introduce genes sco0958 andsco5888 into Streptomyces hosts GAL1001, GAL4111 and G011. In Example 2Table 3 shows the codes used for the genetically modified strains. Allthe strains produced more lipids as compared to the parent strains. Thecultivations were carried out in temperatures ranging from 20 to 36° C.,agitation varying from 0 to 800 rpm, and pH 5-8.5.

The GMO strains G009, G010, G013, G014, G015, G012, G016, G017, and G019with their parent strains, GAL1001, GAL4111 and G011, as controls werecultivated in a wide variety of cultivation media. The lipid yield wasestimated as (g_(lipids)/g_(lucose))*100. The parent strains GAL1001 andG011 produced lipids as estimated by dry mass of chloroform extracts andby TLC analysis referring to standards to be 0.1-0.5 g/l of thecultivation broth, respectively. The chloroform extracts of cellfractions of the transformants gave a mass in the range of 5.9-25.2 g/lwhile the TAG content was estimated as 3 to 23 g/l, The best improvementwas obtained by G009. Surprisingly, the lipid fraction on TLC was verysimilar in all trans-formants and >70% of detectable lipids was in TAGfraction.

In the above calculations the sugar content was calculated to be 10 g/lin the tested media containing Corn Steep Liquor 20 g/l, Nutrisoy 10 g/land Dextrose syrup 10 g/l. The cultivations were carried out in flasksfor 5 days at 28° C., 150 rpm, lipids were extracted from the cells andsupernatant separately with equal volume of chloroform-Methanol (2:1) byshaking for 1 hour. A sample of chloroform fraction was applied on TLCplate and a chloroform fraction was evaporated to dryness for massdetermination.

In order to the lipid composition obtained to be suitable for furtherprocessing in the manufacture of biofuel, the chemical nature of thesecompounds is critical. Though different forms of fats are suitable forchemical processing for biofuel production the preferred compounds areTAGs. There are several known methods to further characterize themetabolites in addition to TLC (thin layer chrometograpghy) analytics,for example GC (gas chromatography). GC analysis can be carried out by astandard procedure (ISO15304). HPLC can be used to determine theglyceride lipid profile of the strains. For example, the lipid profilecharacteristic to a parent strain (exemplified by GAL1001) and to agenetically modified strain (exemplified here by G009) is given in theTable 2.

TABLE 2 Glyceride profile of lipids as percentage value derived fromGAL1001 and G009 as analyzed by HPLC. The nature of lipids GAL1001 G009TAGs 95 88.6 Oligomers N.A. 5.2 Diacylglycerols N.A: 4.3Monoacylglycerols N.A. 0.3 Free fatty acids  5 1.7 *N.A. = not available

Majority of Lipids in Streptomycetes Consisted of Triglycerides,

TABLE 3 Examples of fatty acid distribution (% from total fatty acids)of S. roseosporus GAL4111 and S. albus GAL1001 as determined by GC-MS.The said strains were cultivated for 2 days in cell waste medium; 10 g/lof CSL and 50 g/l of cell waste (cell debris of streptomycetes) withoutadditional supplements at 28° C., 150 rpm. GAL4111 GAL1001 n-C10:0 0.020.03 n-C10:1 0.01 0.00 iso-C11:0 0.03 0.00 anteiso-C11:0 0.06 0.00n-C11:0 0.05 0.07 iso-C12:0 0.23 0.28 anteiso-C12:0 0.09 0.09 n-C12:00.11 0.12 iso-C13:0 0.25 0.29 anteiso-C13:0 0.45 0.55 n-C13:0 0.15 0.10n-C13:1 0.00 0.00 iso-C14:0 6.41 7.32 anteiso-C14:0 0.27 0.33 n-C14:01.25 1.03 n-C14:1 0.06 0.00 iso-C15:0 3.94 4.34 anteiso-C15:0 13.2014.66 n-C15:0 N.A. N.A. n-C15:1 0.85 0.30 iso-C16:0 16.98 18.65anteiso-C16:0 0.11 0.13 n-C16:0 14.78 14.30 n-C16:1 4.05 2.79 iso-C17:01.40 1.37 anteiso-C17:0 4.67 4.92 n-C17:0 0.61 0.58 n-C17:1 3.40 3.43iso-C18:0 0.29 0.25 n-C18:0 1.78 1.54 n-C18:1 8.52 8.44 n-C18:2 13.0611.43 n-C18:3 0.79 0.63 n-C19:1 0.47 0.46 n-C20:0 0.20 0.19 n-C22:0 0.710.99 n-C23:0 0.31 0.19 n-C24:0 0.14 0.12 Fatty alcohols 0.12 0.09 Otherfatty 0.18 0.00 acids * N.A. = Not available

Streptomycetes oil was saturated and majority of fatty acids determined(˜70%) were saturated. Further, Streptomycetes oil contained significantcontent of methyl-branched fatty acids (45 to 50% in this case).

TABLE 4 Example of lipid composition of S. roseosprous GAL4111 and S.albus GAL1001 as determined by GC-MS. GAL4111 GAL1001 Fatty acids* 84.889.5 Fatty alcohols 0.3 0.1 Squalenes 4.3 2.5 Other lipids 0.2 0.0Unidentified lipids 10.3 7.9 *Fatty acids include the acylglycerols andfree fatty acids

Majority of the lipids consisted of fatty acids (included inacylglycerols and free fatty acids). Lipids also contained squalenes(2.5 and 4.3% from total lipids).

Squalenes in GAL4111 and GAL1001 composed of squalene,tetrahydrosqualene, dihydrosqualene, (main components),hexahydrosqualene and octahydrosqualene.

According to the present invention, there are several alternatives tocultivate the suitable Streptomyces strains for accumulation of lipids.Different conditions including variety of carbon and/or nutrientsources, and growth conditions were tested.

In order to have an industrially feasible process, the strains naturallyaccumulating lipids, such as G009, G013 and G017, shall be suitable foraerobic fermentation and fermentation process should be cost-efficient.The costs of fermentation process are heavily affected by mediacomponents, energy consumption, waste costs and manpower.

Though it is possible to use the medium derived from pure ingredientsand for example those described herein, TSB, 2*TY, and E05, it is morecost-efficient to select any waste fraction without separation,hydrolysis, and/or purification of components as raw materials. Therequirements are that the bacteria in use are rich in digestive enzymesto facilitate the growth by crude ingredients including in waste.Therefore, the present invention further contemplates the use ofindustrial waste fraction or a combination of pure ingredients with thewaste. As described herein a comprehensive test series was done with awide variety of organic wastes or residues from industry includingagriculture, municipal waste and microbial residue. Methods suitable foruse in the present invention for generating free sugars and a source ofnutrient to be utilized for growth from waste fractions are those thatare generally known such as use of suitable enzymes for digesting ofcrude ingredients. However, cultivation of bacteria possessing thesedigestive enzyme functions while having capabilities for accumulation ofsaid lipids are preferable. Suitable strains for this purpose areconsequently S. roseosporus and S. albus strains. Preferred strains areG009, G010, G013, G014, G015, G012, G016, G017 and G019 with theirparent strains, GAL1001, GAL4111 and G011.

The strains involved in this disclosure and preferably the strains G009,G010, G013 and G017 may be cultivated on the organic waste(s) orresidue(s). The uses of cell debris derived e.g from the foregoing lotare very suitable nutrient sources to produce lipids in a cost-efficientway. In these cultivations the changes in cell mass were detected tolower in the first two to three days increasing 5-20 g/l in thefollowing three to four days. The dry mass of chloroform extractsderived from these cultivations were in the range of 7-65 g/l reflectingthe amount of TAGs as 3-23 g/l as analysed on TLC.

All those unit operations and raw materials described in the embodimentsof the present invention, either alone or in combination are efficientin production of oils for biofuels. In specific preferred embodimentsthe process uses strains G009, G010, G013 or G017. The inoculation ispreferably carried out by using spores.

The amount of spores is advantageously about 10¹⁰ spores/1 litre to5*10¹² spores/500 litre. The cultivation is preferably carried out for 2to 6 days. The cultivation temperature is about 28° C. The cultivationis carried out as a batch or fed-batch fermentation. Suitable agitationis used during cultivation. Furthermore, it is recommended to usepasteurization of medium instead of sterilization to avoid high energyconsumption. The process can be continued, for example, for 6 dayswithout any supplements or lipase inhibitors, such as silver ions addedin low concentration at the 6^(th) day of cultivation. In the end of thecultivation the cell mass is harvested. It is typically about 65 kg/500l batch. The lipids are recovered from the cell biomass or culture brothby a suitable method. The yield with solvent based extract or byphysical scattering is typically at least 5 kg TAGs per 1000 litre spentcultivation medium, typically 10 to 70 kg TAGs per 1000 litre, usuallyabout 30 kg of TAGs from 1000 l batch.

Recovery of Oil

In various embodiments of the invention, oil, or precursors for oil, maybe recovered from cell biomass or culture broth using any method knownin the art or developed in the future. For example, bacteria may beseparated from the medium using a filtration or decanting techniques.Alternatively, centrifugation with industrial scale commercialcentrifuges of large volume capacity may be used to separate the desiredproducts.

In some embodiments of the invention, bacterial cells may be disruptedto facilitate the separation of oil and other components. Any methodknown for cell disruption may be used, such as ultrasonication, osmoticshock, mechanical shear force, cold press, thermal shock,enzyme-catalyzed or self-directed autolysis. Oil can be recovered fromcells by extraction with organic solvents or by any method known in theart or developed in the future.

The strains, methods, cultivation conditions, ingredients forfermentation and the process scheme disclosed and claimed herein concerntechnology that supports large scale and economical cultivation ofStreptomyces bacteria. This technology is useful to support industrialmanufacturing of the various related products. This technology may be ofuse to economically support the massive cultivation and harvesting ofstreptomycetes.

Production of Biofuel

The lipids produced with the method described herein can be used asfeedstock for the production of biodiesel, renewable diesel, jet fuel orgasoline. Biodiesel consists of fatty acid methyl esters, and istypically produced by transesterification. In transesterification, theacylglycerols are converted to long-chain fatty acid alkyl (methyl,ethyl or propyl) esters. Renewable diesel refers to fuel which isproduced by hydrogen treatment (hydrogenation or hydroprocessing) oflipids. In hydrogen treatment, acylglycerols are converted tocorresponding alkanes (paraffins). The alkanes (paraffins) can befurther modified by isomerization or by other process alternatives.Renewable diesel process can also be used to produce jet fuel and/orgasoline. In addition, cracking of lipids can be performed to producebiofuels. Further, lipids can be used as biofuels directly in certainapplications.

The Streptomyces lipids are beneficial for the production of biofuel.Streptomyces fatty acids typically contain methyl-branched chain fattyacids, which are beneficial for biofuel and lubricant applications.Branched fatty acids have a broader liquidity range, making them ofinterest for low-temperature applications and their low surface tensioncauses good spreadability (Gunstone et al. 2007). Fatty acid branchingimproves the cold properties of biofuels, such as biodiesel or renewablediesel. The Streptomyces oil has relatively high saturation degree(contains high amounts of saturated fatty acids). This property is anadvantage especially for the renewable diesel process, since fatty acidsaturation decreases the amount of hydrogen needed in hydrogenation.High saturation degree of lipids may also improve the stability andstorability of oil, and reduce the need of antioxidants in oil storage.Further, the main fatty chain lengths are mainly from C14 (14 carbons)to C18 (18 carbons), which is advantageous for the utilization in dieselapplications.

Lipids produced with the method can be used as base oils for lubricants(lubrication oils) or as a starting material for production of base oilsfor lubricants. Streptomyces oil contain squalene or squalene derivates(Gräfe et al. 1985; Olukoshi and Packter 1994). Especially, squalene andsqualene derivates are suitable for uses in lubricant applications.However, other lipids by Streptomyces can be used for lubricantapplications as well.

Biofuel which comprises the lipid composition produced according to thepresent disclosure may comprise advantageous properties for biofuel use.Such properties include for example fatty acid branching which improvescold properties.) Fatty acid saturation is advantageous especially forrenewable diesel production.

Deposited Microorganisms

Streptomyces sp. G011 strain was deposited under Budapest Treaty on 15Dec. 2009 to DSMZ-Deutsche Sammlung fur Mikroorganismen and ZellkulturenGmbH, and it received the Accession number DSM 23182. Biologicalmaterial deposited under accession number DSM 23182 at DSMZ-DeutscheSammlung fër Mikroorganismen and Zellkulturen GmbH by Galilaeus Oy ofKairiskulmantie 10, 20781 Kaarina, Finland. Galilaeus Oy authorises theapplicant to refer to the aforesaid biological deposit in the presentapplication and applications/patents claiming priority from thisapplication, and gives his unreserved and irrevocable consent to thedeposited material being made available to the public in accordance withthe applicable national laws.

The other strains presented herein show identical features to thestrains available in commercial culture collections as shown in Table 5.The strains as listed in Table 5 were first identified according totheir secondary metabolites when available, a partial sequence of16SrDNA and by comparison of colony morphology. The sequence identity ofGAL1001, GAL1002, GAL1003, GAL4051, GAL1004, GAL1005, GAL4111, GAL1006,GAL1007, GAL4081, GAL4082 in the DNA fragment of about 1.4 kb hasbeen >98% to the corresponding sequences of the Strains indicated inTable 5. The sequences used in comparison are found in Gene Banks.

Table 5 Shows Identification of the Strains

Corresponding Galilaeus' Strain with collection 16S ribosomal 16Sribosomal code Strain number RNA gene code RNA gene length GAL1001 S.albus DSM 40313 GI: 219878476 1499 bp GAL1002 S. lividans NRRL B16148GI: 66379295 1449 bp GAL1003 S. coelicolor DSM 40233 GI: 220961405 1396bp GAL4051 S. hygroscopicus NRLL 5491 GI: 228480526 1385 bp GAL1004 S.aureofaciens DSM 40731 GI: 284022440 1402 bp GAL1005 S. griseus ATCC13273 GI: 196128028 1428 bp GAL4111 S. roseosporus NRRL 11379 GI:195979310 1431 bp GAL1006 S. avermitilis NRRL 8165 GI: 162960844 1529 bpGAL1007 S. lydicus ATCC 25470 GI: 219846852 1481 bp GAL4081 S. peucetiusP55 comparable to S. peucetius GI: 219857135 1486 bp P55#SnorO; DSM19075 GAL4082 S. peucetius D2 * GI: 219857135 1486 bp GAL4211 S.milbemycinius NRRL5739 GI91178060 1457 bp * Studies on a second andthird ring cyclization in anthracycline biosynthesis. J. Anti-biot(Tokyo), 2003 Feb; 56(2): 143-53

The strains were identified with 16SrDNA sequences obtained by PCR usingthe homologous primers:

UNIfor 5′ GGTGGAGCATGTGGTTTA 3′ (SEQ ID NO: 5) UNIrev 5′CCATTGTAGCACGTGTGT 3′ (SEQ ID NO: 6)

Various embodiments of the invention are described below with the aid ofthe following numbered clauses 1-36:

1. A process for producing lipids for biofuel or lubricant, whichcomprises

-   -   cultivating bacterial cells of the genus Streptomyces in a        medium comprising organic waste(s) or residue(s) or mixtures        thereof as carbon and/or nutrient source(s);    -   recovering the lipids from the cells or from the culture medium.        2. The process according to clause 1, wherein the organic        waste(s) or residue(s) or mixtures thereof are used as main        source(s) of carbon and/or nutrient.        3. The process according to clause 1 or 2, wherein the amount of        waste or residue in the cultivation medium is 1 g/l to 600 g/l,        typically 1 g/l to 400 g/l, usually 2 g/l to 400 g/l, typically        2 g/1 to 200 g/l.        4. The process according to any one of clauses 1 to 3, wherein        the organic waste(s) or residue(s) comprise(s) industrial        organic waste(s) or residue(s), agricultural organic waste(s) or        residue(s), municipal waste(s) or microbial waste(s) or        residue(s), or any mixtures thereof.        5. The process according to any one of clauses 1 to 4, wherein        the cultivation medium comprises as an additional carbon source        glycerol, a fraction from sugar or starch industry, sugar or        starch syrup(s) or purified sugar(s) or any mixtures thereof.        6. The process according to any one of clauses 1 to 5, wherein        the ratio of waste or residue to starch syrup or sugar syrup is        10/1 to 1/2, preferably 5/1 to 1/1.        7. The process according to any one of clauses 1 to 6, wherein        the amount of triacylglycerols in the spent culture medium is at        least 1 g/litre, preferably 5 g/litre.        8. The process according to any one of clauses 1 to 7, wherein        the produced lipids comprise mainly triacylglycerols.        9. The process according to any one of clauses 1 to 8, wherein        the produced lipids are transesterified to produce biodiesel or        hydrogen treated to produce renewable diesel.        10. The process according to any one of clauses 1 to 9, wherein        the cultivation medium is not sterilized or is pasteurized.        11. The process according to any one of clauses 1 to 10, wherein        the cultivation medium comprises lipase inhibitors.        12. The process according to any one of clauses 1 to 11, wherein        the cultivation is carried out as a batch or as a fed-batch        fermentation.        13. The process according to any one of clauses 1 to 10, wherein        the Streptomyces species is selected from the group of        Streptomyces roseosporus, Streptomyces griseus, Streptomyces        albus, Streptomyces peucetius, Streptomyces aureofaciens        Streptomyces lividans, Streptomyces coelicolor, Streptomyces        hygroscopicus, Streptomyces avermitilis, Streptomyces        milbemycinius and Streptomyces lydicus.        14. The process according to clause 13, wherein the Streptomyces        strain is selected from the group of Streptomyces roseosporus        GAL4111, Streptomyces roseosporus G011, Streptomyces griseus        GAL1005, Streptomyces albus GAL1001, Streptomyces peucetius D2,        GAL4082, Streptomyces peucetius P55 GAL4081, Streptomyces        aureofaciens GAL1004, Streptomyces lividans GAL1002,        Streptomyces coelicolor GAL1003, Streptomyces hygroscopicus        GAL4051, Streptomyces avermitilis GAL1006, Streptomyces        milbemycinius GAL 4211 and Streptomyces lydicus GAL1007.        15. The process according to any one of clauses 1 to 14, wherein        the Streptomyces host is genetically modified to express an        endogenous or exogenous gene encoding DGAT (EC 2.3.1.20) and/or        3-ketoacyl-acyl carrier protein synthase UI (FabH) (EC:        2.3.1.41).        16. The process according to any one of clauses 1 to 15, wherein        the Streptomyces host is genetically modified to express one or        more of genes selected from the group of        (a) sco0958 (SEQ ID NO:1) and/or sco5888 (SEQ ID NO:2);        (b) the closest homologue of said genes in a Streptomyces        species;        (c) a nucleotide sequence which hybridizes to at least one of        said genes or said homologues at 65° C. in 1.5 mM sodium        citrate, pH 7.0 and 0.015 NaCl;        (d) a nucleotide sequence causing the same or an equivalent        function as gene products ID 101096381 or ID 101101330 have;        (e) a nucleotide sequence encoding an amino acid sequence        showing at least 60% identity to SEQ ID NO: 3 or SEQ ID NO:4.        17. The process according to any one of clauses 1 to 16, wherein        the Streptomyces host is made deficient in producing bioactive        metabolites, such as antibiotic agents.        18. The process according to any one of clauses 1 to 17, wherein        the Streptomyces strain is selected from the group of G009,        G010, G013, G014, G015, G012, G016, G017, and G019.        19. A Streptomyces culture for lipid production, which comprises        (a) a population of bacteria of the genus Streptomyces; and        (b) a culture medium comprising organic waste(s) or residue(s)        or mixtures thereof as carbon and/or nutrient source(s).        20. The culture according to clause 19, wherein the organic        waste(s) or residue(s) or mixtures thereof are used as main        source(s) of carbon and/or nutrient.        21. The culture according to clause 20, wherein the amount of        triacylglycerols in the spent culture medium is at least 1        g/litre, preferably 5 g/litre.        22. The process according to clause 20 or 21, wherein the        produced lipid fraction comprises mainly triacylglycerols.        23. The culture according to any one of clauses 20 to 22,        wherein the cultivation medium comprises lipase inhibitors.        24. The culture according to any one of clauses 20 to 23,        wherein the cultivation medium is not sterilized or is        pasteurized.        25. The culture according to any one of clauses 20 to 24,        wherein the Streptomyces species is selected from the group of        Streptomyces roseosporus, Streptomyces griseus, Streptomyces        albus, Streptomyces peucetius, Streptomyces aureofaciens        Streptomyces lividans, Streptomyces coelicolor, Streptomyces        hygroscopicus, Streptomyces avermitilis, Streptomyces        milbemycinius and Streptomyces lydicus.        26. The culture according to clause 25, wherein the Streptomyces        strain is selected from the group of Streptomyces roseosporus        GAL4111, Streptomyces roseosporus G011, Streptomyces griseus        GAL1005, Streptomyces albus GAL4001, Streptomyces peucetius D2,        GAL4082, Streptomyces peucetius P55 GAL4061, Streptomyces        aureofaciens GAL1004, Streptomyces lividans GAL1002,        Streptomyces coelicolor GAL 1003, Streptomyces hygroscopicus        GAL4051, Streptomyces avermitilis GAL1006, Streptomyces        milbemycinius GAL4211 and Streptomyces lydicus GAL1007.        27. The culture according to any one of clauses 20 to 26,        wherein the Streptomyces host is genetically modified to express        at least one gene of the lipid synthesis pathway.        28. The process according to any one of clauses 20 to 27,        wherein the Streptomyces host is genetically modified to express        an endogenous or exogenous gene encoding DGAT (EC 2.3.1.20)        and/or 3-ketoacyl-acyl carrier protein synthase III (FabH) (EC:        2.3.1.41).        29. The process according to any one of clauses 20 to 28,        wherein the Streptomyces host is genetically modified to express        one or more of genes selected from the group of        (a) sco0958 (SEQ ID NO:1) and/or sco5888 (SEQ ID NO:2);        (b) the closest homologue of said genes in a Streptomyces        species;        (c) a nucleotide sequence which hybridizes to at least one of        said genes or said homologues at 65° C. in 1.5 mM sodium        citrate, pH 7.0 and 0.015 NaCl;        (d) a nucleotide sequence causing the same or an equivalent        function as gene products ID 101096381 or ID 101101330 have;        (e) a nucleotide sequence encoding an amino acid sequence        showing at least 60% identity to SEQ ID NO: 3 or SEQ ID NO:4.        30. The culture according to any one of clauses 20 to 29,        wherein the Streptomyces host is deficient in producing        bioactive metabolites, such as antibiotic agents.        31. The culture according to any one of clauses 20 to 30,        wherein the Streptomyces strain is selected from the group of        strains G009, G010, G013, G014, G015, G012, G016, G017, and        G019.        32. A Streptomyces host genetically modified to express an        endogenous or exogenous gene encoding DGAT activity (EC        2.3.1.20) and/or 3-ketoacyl-acyl carrier protein synthase III        (FabH) (EC: 2.3.1.41), or a nucleotide sequence causing the same        or an equivalent function as gene products ID 101096381 or ID        101101330 have.        33. The host according to clause 32, wherein host cell is        selected from the group of species of Streptomyces roseosporus,        Streptomyces griseus, Streptomyces albus, Streptomyces        peucetius, Streptomyces aureofaciens, Streptomyces lividans,        Streptomyces hygroscopicus, Streptomyces avermitilis,        Streptomyces lydicus, preferably selected from the group of        species comprising Streptomyces roseosporus, Streptomyces        milbemycinius and Streptomyces albus,        34. The host according to clause 32 or 33, wherein the host is        genetically modified to express one or more of genes selected        from the group of        (a) sco0958 (SEQ ID NO:1) and/or sco5888 (SEC) ID NO:2);        (b) the closest homologue of said genes in a Streptomyces        species;        (c) a nucleotide sequence which hybridizes to at least one of        said genes or said homologues at 65° C. in 1.5 mM sodium        citrate, pH 7.0 and 0.015 NaCl;        (d) a nucleotide sequence causing the same or an equivalent        function as gene products ID 101096381 or ID 101101330 have;        (e) a nucleotide sequence encoding an amino acid sequence        showing at least 60% identity to SEQ ID NO: 3 or SEQ ID NO:4.        35. The host according to any one of clauses 32 to 34, wherein        the strain is selected from the group of strains G009, G010,        G013, G014, G015, G012, G016, G017, and G019.        36. A lipid composition produced according to any one of clauses        1 to 15.        37. Use of the lipids or lipid composition produced according to        any one of clauses 1 to 15 or the lipid composition according to        clause 36, or a fraction of the lipids or lipid composition as        biofuel and/or lubricant, or as a starting material for biofuel        and/or lubricant production.        38. Use of the lipids or lipid composition produced according to        any one of clauses 1 to 15 or the lipid composition according to        clause 36 s for the production of biodiesel or renewable diesel.        39. Biofuel which comprises the lipids or lipid composition        produced according to any one of clauses 1 to 15, or the lipid        composition according to clause 36, or a fraction of lipids or        lipid composition, and optionally suitable additives for biofuel        use.        40. Lubricant which comprises the lipids or lipid composition        produced according to any one of clauses 1 to 15, or the lipid        composition according to clause 36, or a fraction of lipids or        lipid composition, and optionally suitable additives for        lubricant use

EXAMPLES

The following methods for analysis were used in the experiments involvedin Examples if not otherwise stated in the text.

Methods:

Detection of wet cell mass: Wet cell mass was measured by taking 10 mlsample of culture broth to a tared Falcon tube and centrifuged for 10minutes at 4000 rpm. After centrifugation supernatant was discarded andFalcon tube was weighted to get mass of cell fraction. The cell mass wasgiven as grams per 1 litre of the culture broth.

Detection of dry cell mass: Wet cell mass was dried at 70° C. for twodays after which mass was determined by weighing. The cell mass wasgiven as grams per 1 litre of the culture broth.

Detection of PMV: Package Mycelia Volume was measured by taking 10 ml ofculture broth and centrifuged for 10 minutes at 4000 rpm after whichvolume of cell phase was measured as % figure.

Visual analysis of culture: The bacterial cultures were visuallyanalysed by separated colonies on agar plate, by studying liquidcultures and by microscopic analysis.

TLC analysis: 5 g/l of ten times concentrated Chloroform extract waspipetted on TLC plate (Silica gel 60 F254 Merck 1.05729) and run inhexane:diethyl ether:acetic acid (80:20:2). Lipids were coloured withiodine after the run or burned to carbon. Burning of lipids wasperformed by dipping the plate in 50% H₂SO₄ and heating the plate 1 hourin 180° C. Cholesterol (C), cholesterol octadecanat (COD), decanoicacid, glyceryl trimyristate (GTM) and L-α-phospatidylethanolamine wereused as standards on TLC. Lipids were visually detected on TLC-plates asyellow (iodine) or black (carbon) spots.

Analysis of TLC spots: Lipids were visually detected on TLC-plates asyellow (iodine) or black (carbon) spots. More clearly iodine colouredspots were seen in UV light. Sample spots were compared with standardsto estimate the quantities in g/l. Values (−, +/−, +, ++, +++ or 0-3)were given based on the intensity of the spots if comparison was madebetween the samples in the same test run.

Also g/l values of TAGS were estimated by image analysis using image Jprogram (http://rsbweb.nih.gov/jj/index.html). The standard curve wasprepared using concentration scale from 1 g/l up to 40 g/l and the titreof lipids in the culture broth was measured against the standard curve.

Sample extraction: The whole culture broth (solid stage cultivations) orseparated mycelia was extracted with an equal volume ofchloroform-methanol (Clf-MeOH; 2:1). Tubes were incubated in a shaker atRT for 1 hour. After centrifugation sample was taken from the extractand analysed by TLC and/or by GC.

Detection of dry extraction weight: Dry extract weight was determined bydrying 1-5 ml of extract at RT for one day in air blow after which masswas determined by weighing. The mass was given as grams per 1 litre ofthe culture broth.

Bioassay for Antibiotic Production:

The indicator microorganism was cultivated in TSB broth at +30° C.overnight. The cell stock was diluted 1:100 (v/v) to TSB soft agar.Equal amounts of TSB soft agar (10 ml) were transferred on top of TSBagar plates and the soft agar layer was let to solidify. Small discs ofthe mutant and control cultures or ethyl acetate extractions (1:1) weretransferred on top of the plates. The plates were incubated at +37° C.overnight. The clear halos formed by the mutants were compared to thecorresponding halos of the control cultivation.

HPLC Method in Brief:

-   -   Equipments:    -   Apparatus: Agilent 1100-series chromatography system (A312-319)    -   Detector: Agilent UV-VIS-detector (G1315A)    -   Column: Zorbax SB-C8, 4.6*150 mm, 3.5 μm    -   Run Parameters:    -   Eluents: Eluent A 2000 ml PW    -   Eluent B 2000 ml MeCN    -   Column temperature: 60° C.    -   Flow rate: 1.5 ml/min    -   Run time: 15 min    -   Injection: 5 μ/l+needle wash (1:1 PW+MeOH)    -   Detection: 240 nm

Time Eluent A Eluent B Flow 0.00 31% 69% 1.5 ml/min 10.00 31% 69% 1.5ml/min 10.01 5% 95% 1.5 ml/min 13.00 5% 95% 1.5 ml/min 13.01 31% 69% 1.5ml/min

Example 1 Screening of Streptomycetes for Accumulation of Lipids

Streptomyces species from the local culture collection (Table 1) weretested for growth on standard cultivation conditions to elucidate thecycle time, cell mass and accumulation of lipids. The strains werecultivated in typical broth, in tryptone soy broth TSB (Difco) for twoto three days in a shaker (100-330 rpm, 26-34° C.). The followingstrains were found to give a high cell mass and accumulation of lipidsin remarkable quantities in the standard cultivation conditions: GAL4111(Streptomyces roseosporus), GAL1005 (Streptomyces griseus), GAL1001(Streptomyces albus) and GAL4082 (Streptomyces peucetius D2).

An aliquot of the spore suspension or a loop of mycelia of each strainwas used to inoculate 50 ml of TSB medium in 250 ml Erlenmeyer flask.Incubation with shaking was allowed to continue for three days and asample of 10 ml was taken in each day of cultivation, e.g. in 24 hoursintervals. The following characters were analyzed: determination of thewet and dry cell mass, PMV, pH follow up and visual analysis by samplingto define the growth cycle, extraction of lipids fraction in chloroformand TLC analysis of the chloroform extracts.

Typical Cultivation Conditions: Temperature: 22-36° C.

pH: 5.0-8.5agitation: 100-330 rpm (¾-1 inch throw)inoculum form: vegetative mycelia, substrate mycelia, sporestransferring rate: 0.5-50%standard medium in use: TSB, 2*TY, E05TSB is Tryptone Soya Broth from Difco containing 17 g/l pancreaticdigest of casein, 3 g/l enzymatic digest of soybean meal, 2.5 g/ldextrose, 5 g/l sodium chloride, 2.5 g/l dipotassium phosphate; 2*TYcontain 16 g/l of tryptone pepton, 10 g/l yeast extract, 5 g/l NaCl, andE05 contains the following ingredients: 20 g/l of dextrose, 20 g/l ofstarch, 5 g/l of farmamedia, 2.5 g/l of yeast extract, 1 g/l of MgSO₄.7H₂O, 1 g/l of KH₂PO₄, 3 g/l of CaCO₃, 3 g/l of NaCl.

Characters of the Streptomyces Culture:

Time for exponential growth: 12-64 hTime to accumulate lipids: 24-64 hThe main fraction of lipids: TAGsThe content of TAG in metabolite fraction as estimated by TLC: 20-80%The oil content in extract as measured by GC is 25-80%, the content ofTAGS is 50-95% in oil fractionThe mass of chloroform extract: >10 g/l of culture brothThe TAG fraction of chloroform extract: 10-80%Wet cell mass: >100 g/lDry cell mass: >8 g/lThe range of PMV: 6-16%Increase of TAGs (highest amount−zero sample) by Image J: 3 g/l (timefor highest value 3 days)

Example 2 Construction of Genetically Modified Strains

Two strains, GAL4111 and GAL1001 were used as the hosts of geneticengineering though the same methods are useful for GAL005 and GAL4082and for several other streptomycetes. In addition, a blocked mutant ofdaptomycin producing GAL4111 was generated to prevent production ofantibiotics in cultivations and designated as G011. Interestingly, allother cultivation properties of G011 were the same as found in GAL4111except the lack of accumulation of lipopeptide antibiotics in detectablequantities in G011. G011 accumulates TAGs and the other lipids insimilar quantities in the same cultivation conditions as GAL4111.

If referred to the standard methods in construction of geneticallymodified strains, these are found in the Streptomyces manual by Kieseret al., 2000 for streptomycetes and in Sambrook and Russell, 2001 for E.coli.

Plasmid Constructions:

The genes that are involved in fatty acid biosynthesis called sco0958and sco5888 were cloned from S. coelicolor genomic DNA into pIJE486vector to give pIJEsco0958 and pIJEsco5888, respectively. Using the samerestriction sites the genes were cloned in a low-copy number vectorpHJL401 to give pHJsco0958 and pIJEsco5888, respectively. Genes werealso combined in same construct to give pIJEsco5888+0958 andpHJLsco0958+5888, respectively. The genes sco5888 and sco0958 wereobtained by PCR using the homologous primers:

Sco5888for (SEQ ID NO: 7) 5′ ATT TCTAGA AAA CCG TCC ATC ACG CGA G 3′        Xba1 Sco5888rev (SEQ ID NO: 8) 5′ATT AAGCTT ACTAGT ATG GTC GTC CTT GGT TCA TC 3′        HindIII SpeI andSco0958for (SEQ ID NO: 9) 5′ ATT TCTAGA ACTAGT GAT CGT ACT TGA CCGTAA TC 3′        XbaI   SpeI Sco0958rev (SEQ ID NO: 10) 5′ATT AAGCTT GCTAGC CGA ACA GCG GAT TTT ATT CAG 3′        HindIII NheI

The fragments obtained by PCR were cloned into the vector pIJE486 usingthe corresponding restriction sites. For introduction of DNA into thestrains GAL4111 and GAL1001, the protoplast transformation was used. Astandard PEG-assisted transformation method was used. Transformationmixtures were plated on R2YE plates and incubated at 30° C. Afterovernight incubation 20 μg/ml thiostrepton in water suspension wasspread on plates for the selection of plasmid containing strains.Incubation was continued for 3-5 days after which the transformants werepicked up from the plates.

The fragments described above were ligated and cloned in E. coli by astandard procedure for transferring into Streptomyces species.

PCR products were verified by sequencing. Plasmids of the transformantswere isolated and digested to verify transformed plasmid.

The following genetically modified strains were created and tested forincreased accumulation of lipids as shown in Table 6.

TABLE 6 The designation of clones used in this invention. Code PlasmidHost strain G009 pIJEsco0958 GAL1001 G010 pIJEsco0958 GAL4111 G013pIJEsco5888 GAL1001 G014 pIJEsco5888 GAL4111 G015 pIJEsco5888 + 0958GAL4111 G012 pIJEsco0958 G011 G016 pHJLsco5888 GAL1001 G017pHJLsco0958 + 5888 GAL1001 G019 pHJLsco5888 G011 pIJE486 is a high copynumber plasmid replicating in streptomycetes (Ylihonko et al., 1996)pHJL401 is a low copy number plasmid replicating in streptomycetes(Kieser et al., 2000)

Example 3 Small-Scale Cultivation of GMO-Streptomycetes for Accumulationof Lipids

The strains G009, G010, G012, G013, G014, G015, G016, G017 and G019 werecultivated in the conditions as described here. The host strains, G011,GAL4111 and GAL1001 were used as controls in cultivations.

Typical Cultivation Conditions: Temperature: 22-36° C.

pH: 5.0-8.5agitation: 0-330 rpminoculum form: vegetative mycelia, substrate mycelia, sporestransferring rate: 0.5-50 G/0medium in use: TSB, E05 as given in Example 1 and different kinds ofwaste or residue medias as described in example 4.

The accumulation of TAG was compared to that of the wild type, GAL1001and GAL4111 by TLC analysis. FIG. 5 demonstrates an example of theaccumulation of TAGs in different media by the strains G017, G016, G013and G011. There was a clear increase in accumulation of lipids andespecially TAGs in the GMO strains carrying the gene sco0958 andincrease in those clones (strains) carrying sco5888 in different plasmidvectors. The results are given here:

TABLE 7 The designation of GMO strains used. Improvement-% Cell mass(wet of TAGs as weight) % increase TAG fraction by compared to the Codeor decrease TLC (g/l) parent. G009 −1% 29 300 G010 −25% 18 50 G013 −77%11 300 G014 +14% 20 11 G015 +12% 25 100 G011 +16% 1 0 G012 −26% 12 30G016 −45% 24 230 G017 +13% 20 300 G019 +121% 17 40

Example 4 Content of the Cultivation Broth: Usage of Waste for Growth

To enhance the maximum growth and accumulation of TAGs in economical,lowcost, cultivation conditions, several waste and/or fractions wereused as carbon and/or nutrient sources in cultivations. Surprisingly,all the tested streptomycetes according to Example 1 and Example 2 wereable to grow and accumulate lipids in a large spectrum of waste. Thewaste fractions were tested alone and with sugar, and in combinationwith other nutrients. The following waste fractions in Table 8 weresuccessfully used as will be indicated by cell growth and accumulationof TAGs. The following data was derived from cultivations of G009 in theeach non-hydrolysed (depolymerized) waste (50 g/l)+dextrose syrup (DX75)(10 g/l).

TABLE 8 The designation of materials mainly wastes or residues used inthis invention as carbon and/or nutrient sources and their influence ongrowth and accumulation of TAGs. Accumulation of lipids (% increase) ascompared Growth in CFU to cultivation In Material (CFU/ml) TSB Bran andchaff 10⁴ +140 Soya 10⁷ +100 Corn steep liquor 10⁶ +150 (CSL) Dextrosesyrup 10⁶ NA Starch syrup NA NA Bacterial cell 10⁷ +94 waste (lipidsextracted) Molasses 10³ +120 Mash 10⁴ +115 Sludge 10³ +20 OVR feed <10 NA Farmamedia 10⁴ +120 Bagasse 10² NA Straw NA +50 Mink feed NA +10Offal 10³ +10 Bone 10⁵ +20 Organic waste 10⁷ +150 (bio waste) vegetablesOrganic waste 10⁴ +146 of garden Organic waste 10⁷ +139 of bakery Algaebiomass 10⁷ +203 * Estimated from 5 days sample-2 days sample

Example 5 Fermentations of the Selected Strains in the ControlledConditions

The strains GAO 001, GAL4111, G009, and G010 were cultivated in thecontrolled fermentation conditions in the following range:

Temperature: 22-36

pH: 5.0-8.5agitation: tip speed of 0-4 m/saeration: 0-2 vvminoculum form: vegetative mycelia, substrate mycelia, sporespassages: 0-2 seedtransferring rate: 0.5-50%volume: 1.5 l working volumeBasic medium: TSB, 2*TY, E05 (the content of these media is given inExample 1, and several waste medias as shown in Table 9.

TABLE 9 Used waste or residue medias in fermentation. CSL, 30 g/l;Dextrose syrup 10 g/l CSL, 5-20 g/l; Meat 15-20 g/l CSL, 5-20 g/l; Oatbran 15-20 g/l CSL, 15 g/l; Dextrose syrup 10 g/l CSL 30 g/l and Offal(class 2) 30 g/l CSL, 10 g/l; Cell waste 50 g/l CSL, 10 g/l; Dextrosesyrup 10 g/l; Cell waste 50 g/l Dextrose syrup 10 g/l; Cell waste 50 g/lCSL 20 g/l, Soya 20 g/l, Dextrose syrup 10 g/l Dextrose syrup 20 g/l,starch or straw or bagasse 20 g/l, bio waste 2.5-50 g/l, algae 50 g/l,MgSO₄•7H₂O1 g/l, KH₂PO₄ 1 g/l, CaCO₃ 3 g/lCharacters of the Streptomyces culture:Time for exponential growth: 12-64 hTime to accumulate lipids: 24-64 hThe main fraction of lipids based on TLC: TAGSThe content of TAG in metabolite fraction as estimated by TLC: >8The mass of chloroform extract: >15 g/l of culture brothThe TAG fraction of chloroform extract: 10-80%Wet cell mass: >200 g/lDry cell mass: >20 g/lThe range of PMV %:10-40Increase of TAGs (highest amount−zero sample) by Image J: 4 g/l (timefor highest value 6 days).

Example 6a Batch Fermentation of the Strain G009

The said strain was cultivated at the fermentation volumes of 1.5, 20and in 500 litre. The following procedure gives detailed information ofthe easily repeatable fermentation process.

Inoculation: spores or a plug of agar plate cultureTransferring rate: 4%Seeding steps: 2

Temperature: 28° C. Aeration: 0.5 vvm Stirring: 100-280 rpm

Back pressure: 0.5 barpH before sterilization: 7Cycle time: 96 hoursSteady state reached: 24 hours (DO is 0 after 24 hour cultivation)Cultivation medium: several waste and/or residue medias as given inExample 5, E05, the ingredients of the basic E05-medium is given hereand the materials that can be used to replace them (Table 10).

TABLE 10 The ingredients that are used to replace basic E05-mediummaterials Ingredient Replaceable g/l dextrose Syrup (5-20 g/l) 20.00starch Bagasse or straw 20.00 farmamedia Bio waste* (2.5-50 g/l), 5.00yeast extract algae debris** (2.5-100 g/l), 2.50 bacterial celldebris*** (50-200 g/l) MgSO₄•7H₂O Essential 1.00 KH₂PO₄ Not essential1.00 CaCO₃ Not essential 3.00 NaCl Not essential 3.00 *= compostablewaste like domestic, bakery, garden, vegetables, brewery (e.g. mash),offal or mixture of these; composition varies **= Phaeodactylum,Chlorella and Dunaliella ***= any cell mass, e.g. lactobacilli andstreptomycetesCell mass (wet): 348 g/l

PMV: 30%

Chloroform extract dried: 28 g/lTAGs obtained based on TLC: 23 g/lTAGs in chloroform extract: 82%Ratio to convert fed sugar to TAGs: from 40 g/l to 23 g/157.5%(additional sugar from waste) (the yield was calculated based on puresugar (dextrose and starch) added only). Theoretical maximum is 33%.Yield higher than theoretical maximum means that lipids are producedfrom sugars included in waste materials. Increase of TAGs (highestamount−zero sample) by Image J: 10.2 g/l (time for highest value 6 days)

Example 6b Batch Fermentation of the Strain GAL1001

The said strain was cultivated at the fermentation volumes of 1.5 l, 20l and in 500 l. The explained procedure given in example 6a givesdetailed information of the easily repeatable fermentation process.

The Indicative Figures of Cultivations:

Cell mass (wet): 267 g/1

PMV: 25%

Chloroform extract dried: 10 g/lTAGs obtained: 5 g/lRatio to convert fed sugar to TAGs: from 40 g/l to 5 g/l=12.5%Increase of TAGs (highest amount−zero sample) by image J: 2.1 g/l (timefor highest value 3 days).

Example 7 Fed-Batch Fermentation of the Strain G009

The said strain was cultivated at the fermentation volumes of 1.5, 20and in 500 litre. Parameters as described in Example 6a. Feeding ofdextrose start after 1-2 days of cultivation, when primary glucose wasmostly consumed, and was continued to the end of cultivation. The amountof fed sugar is 40 g/l as a total so total amount of sugar added toculture broth was 60 g/l.

The Results Per One Litre of the Culture Broth Obtained in 4-DaysFermentations:

Cell mass (wet): 356 g/l

PMV: 36%

Chloroform extract dried: 1.4 g/lTAGs obtained: 6 g/l

Ratio to convert fed sugar to TAGs: from 60 g/l to 6 g/l=10% Increase ofTAGs (highest amount zero sample) by Image J: 3.6 g/l (time for highestvalue 3 days)

The examples indicates that fed-batch cultivation can be used in thelipid production by Streptomyces.

Example 8 Combination of Different Waste in Broth; Algae and Biowaste

The strain G009 was cultivated in the controlled conditions in a brothmade by combining different type of waste and in the followingparameters:

Temperature: 28° C.

pH: 7 in the beginning of cultivationagitation: 300 rpmaeration: 0.5 vvminoculum form: vegetative mycelia, substrate mycelia, sporespassages: 2transferring rate: 2%volume: 1.5 L working volume

TABLE 11 Used wastes and/or residues in fermentation. biowaste(bakery&vegetables (50:50), content not defined; 10 g/l algae(Dunaliella) 50 g/l main sugar source: bagasse sugar (total) 40 g/l(dextrose syrup and starch/bagasse/straw)

Characters of G009 Culture:

Time for exponential growth: 97 hTime to accumulate lipids: 144 hThe main fraction of lipids: TAGsThe content of TAG in metabolite fraction as estimated by TLC: >70% %FIG. 4 demonstrates the accumulation of TAGs in different media by G009.The mass of chloroform extract: >22 g/l of culture broth The TAGfraction of chloroform extract 68.9%TAGs as determined by ImageJ: 15.3 g/l

PMV: 39%

Lipid yield (total fed pure sugar without waste): 55%Increase of TAGs (highest amount−zero sample) by Image J: 4.6 g/l (timefor highest value 3 days)

The example indicates that various wastes and residues can be providedas mixes in the lipid production by Streptomyces. Lipid yield exceededtheoretical value of 33% indicating that sugars are used from waste.

Example 9 Reuse of Lipid-Extracted Bacterial Cultures as Nutrient Sourcein Fermentation

The strains G016, G013 and G009 were cultivated in the controlledconditions in 1.5 liter batch fermentation. The cells were harvested byfiltration and extracted by the equal volume of chloroform (1:1). Afterthat the remaining cell debris was further dried to remove chloroformresiduals at 60° C. for 10 min to be supplied to fermentation mediumwith or without additional sugar sources, such as dextrose syrup 10 g/l.

Temperature: 22-36° C.

pH: 5.0-8.5agitation: tip speed of 0-4 m/saeration: 0-2 vvminoculum form: vegetative mycelia, substrate mycelia, sporespassages: 0-2 seedtransferring rate: 0.5-50%volume: 0.05-1.5 l working volume

Characters of G016 Culture:

Time for exponential growth: 20-144 h

PMV: 33%

Time to accumulate lipids: until 72 hoursThe main fraction of lipids: TAGsThe content of TAG in metabolite fraction as estimated by TLC: >80%The mass of chloroform extract: 27.4 g/lTAGs calculated from quantity in chloroform extract: 14 g/lLipid yield (from total sugar without waste): 51%Increase of TAGs (highest amount−zero sample) by Image J: 1.6 g/l (timefor highest value 3 days)

Characters of G013 Culture:

Time for exponential growth: 20-144 h

PMV: 33%

Time to accumulate lipids: until 144 hoursThe main fraction of lipids: TAGsThe content of TAG in metabolite fraction as estimated by TLC: >80%The mass of chloroform extract: 20.5 g/lTAGs calculated from quantity in chloroform extract: 10 g/l Lipid yield(from total sugar without waste): 49%Increase of TAGs (highest amount−zero sample) by Image J: 2.6 g/l (timefor highest value. 3 days)

Characters of G009 Culture:

Time for exponential growth: 6-50 h

PMV: 20%

Time to accumulate lipids: until 48 hoursThe main fraction of lipids: TAGSThe content of TAG n metabolite fraction as estimated by TLC: >90%The mass of chloroform extract: 14 g/lTAGs calculated from quantity in chloroform extract: 7.0 g/lLipid yield (from total sugar without waste): 50%Increase of TAGs (highest amount−zero sample) by Image J: 3 g/l (timefor highest value 3 days)

The example indicates that lipid extracted Streptomyces cells can bere-used as a nutrient source in lipid production by Streptomyces.

Example 10 Pasteurize Ion of Media

In parallel with the typical fermentation scheme, the cultivationwithout sterilization of the used broths was carried out. Thesterilization at 121° C. for 20 minutes was replaced by warming up to60° C. 10-30 min and 75° C. for 2-10 minutes of both seed and productionbroths. The cultures were daily studied by microscopy and by plating asample of 100 μl on ISA (Tryptone Soya agar) plates allowing the growthof a large spectrum of microbes. Typically no contaminations were foundin the cultures even with shortest heating time and the cultivationswere similar to parallel cultivations in sterile media.

Inoculation: Spores or a Plug of Agar Plate Culture

Transferring rate: 4%Seeding steps: 2

Temperature: 28° C. Aeration: 1 vvm

Stirring: tip-speed 1.3 m/sBack pressure: 0.5 barpH before sterilization: 7Cycle time: 96 hoursSteady state reached: 16 hoursCultivation medium: several waste medias as given in Example 5, E05, 20g/l offal+20 g/l dextrose syrup.

Results:

Cell mass (wet): 178 g/l PMV: 16%Time to accumulate lipids: until 72 hoursThe mass of chloroform extract: 9 g/lTAGs obtained (estimated by TLC): 5 g/lTime to accumulate lipids: until 96 hoursThe main fraction of lipids: TAGsThe content of TAG in metabolite fraction as estimated by TLC: >90%Increase of TAGs (highest amount−zero sample) by Image J: 1.8 g/l (timefor highest value 6 days)

The results indicate that the sterilization of medium can be replaced bymedium pasteurization for lipid production by Streptomyces.

Example 11 Determination of the Cell Growth for Lysis

In the cultivation conditions described in Examples 1-7 above, thesteady state was typically reached in 10-48 hours incubation. Thestationary stage continues for about 48-72 hours after which the celllysis took place. TAGs disappear at prolonged cultivation. Only minorquantities of TAGs—if any—were detectable on TLC in samples derived from7-days culture broths. The lipids and especially TAGs decreasedgradually already on the 4^(th) cultivation day as was detected by TLC.Cell lysis may have liberated the action of lipases resulting inhydrolysis of TAGs as was seen in the cultivation experiments.Therefore, the fermentation was stopped before autolysis or an inhibitorof lipases was added to the culture broth.

Example 12 Prevention of TAG Degradation

The spores of the strain G009 were cultivated in the medium containingthe following raw materials in 1 L of tap water, pH 7: Dextrose 75 20 g,Bagasse 20 g, Biowaste from bakery and garden (1:1) 5 or 10 g, Algae 25to 50 g, MgSO₄.7 H₂O 1 g, KH₂PO₄ 1 g and CaCO₃ 3 g. The cultivationconditions were 28° C., 300 rpm for 11 days. After 6 days ofcultivations, 0.05 g/l AgNO₃ or 0.4% of TritonX100 solution containing0.05 g/l of CaCO₃. The flasks without the said supplements wereconsidered as controls for lipase inhibition treatment study.Cultivation was continued in the same conditions for 5 days more.

The samples were taken after 7, 8 and 11 days of cultivations accordingto the general sampling protocols used in this invention and the resultsof sampling are shown here. The parallel cultivations were done with twoconcentrations of both algae debris and biowaste and the upper row ofeach test condition gave a result with higher concentration of bothwaste fractions.

TABLE 10 The results of lipase inhibition test Weight of ChloroformQuantity of extract (g/l) TAGs g/l by Image J The supplements 7 day 11day 7 day 8 day 11 day No; control 7.6 6.1 5 4.9 0.5 AgNO₃ 7.7 8.5 4.84.8 4.8 TritonX100 + 10.3 10.1 5 5 4.9 CaCO₃

The effect of lipase inhibitors was very well seen in the mass of lipids(chloroform extract) which was slightly increasing or stabile. Theremarkable difference in changes of quantity of TAGs as compared tocontrol was noticed.

Example 13 Generation of Non-Producing Mutants by Random Methods Using aChemical Mutagen

There are several possibilities to generate blocked mutants from anantibiotic producer strain. In this example strain S. milbemyciniusGAL4211, producing an anti-biotic called Milbemycin was used for NTGmutagenesis. The strain was plated on thick ISP4 agar plate (9 cm) andincubated at 30° C. until spores were formed. The spores were suspendedto 10 ml water and transferred to centrifuge tube for shaking smoothly.A homologous suspension of spores was filtered through a 3 cm cottonwool and centrifuged 3000 rpm, 10 min. The harvested spores were storedin 20% glycerol at −80° C. and the spore titre was determined by platingsuitable dilutions on agar plates for colony counting.

The spore suspension with the content of 10⁷ spores 1 ml was treated byNTG, (N-methyl-N′-nitro-N-nitrosoguanidine) at different concentrationof 1-3 mg/ml in pH buffers of 7-9 at +30° C. for 0.5-1 h. AfterNTG-treatment, the cells were washed twice and plated on ISP4 plates.Killing rates observed in the said conditions were 90-100%.

The colonies failed to produce antibiotics as was tested byantibacterial assay and by HPLC (240 and 430 nm) analysis were studiedfor accumulation of lipids.

Example 14 Generation of Non-Producing Mutants by Targeted Inactivatingof the First Biosynthetic Genes

The polyketide biosynthesis (PKS) genes were cloned by PCR usingheterologous but conservative DNA fragment. The fragment was isolatedand cloned into a vector pUC19 replicating in E. coli but not instreptomycetes. A biomarker, a gene encoding apramycin resistance wasinserted in the PKS gene to cause a truncation of the gene product. Therecombinant pUC19 construct obtained was introduced into S.milbemycinius by conjugation. The clones were studied for expression ofantibacterial properties and analyzed for production of milbemycins byHPLC. The verification for non-producing of characteristic antibiotic,milbemycins was done by repeated cultivations in liquid medium and onsolid agar.

Primers used: (SEQ ID NO: 11) forward: 5′ TSGCSTGCTTGCTTCGAYGCSATC-3′(SEQ ID NO: 12) reverse: 5′ TGGAANCCGCCGAABCCGCT-3′

Degenerated primer symbols: S═C or G; Y═C or T; B=C, G or T and N=A, T,C or G.

PCR Conditions:

Number Cycle step Temperature Time of cycles Initial 98° C.  3 min 1denaturation Denaturation 98° C. 30 s 30 Annealing 60° C. 30 s Extension72° C. 30 s Final extension 72° C. 10 min 1

Conjugation:

For conjugation the recombinant pUC19 construct were transformed intoEmil strain ET12567/pUZ8002. A colony was inoculated into 3 ml LB or2×TY containing kan, cam and apr and grown overnight at 30° C., 330 rpm.Overnight culture was diluted 1:30 in fresh LB or 2×TY containingantibiotics and grown at 30° C. to an OD₆₀₀ of 0.4-0.6. Cells werewashed twice with an equal volume of media and re-suspended to 0.1volume of used media. 1 ml of spore suspension of S. milbemycinius withthe content of 10⁷ spores/ml was washed twice with an equal volume ofTSB and re-suspended to 1 ml of TSB. 100 μl or 250 μl of sporesuspension was added 400 μl or 250 μl E. coli suspension and mixed. 100μl of suspension was plated on four MS+10 mM MgCl₂ plates and incubatedat 30° C. 16-20 h. Conjugants were selected by resistance against anantibiotic (apramycin 50 mg/l) and nalidixic acid (1 mg/plate) was usedto kill E. coli. Antibiotics were suspended in sterile purified waterand overlaid on plates.

Example 15 A Blocked Mutant Derived from the Strain Streptomycesmilbemycenius and Accumulating Enhanced Quantities of Lipids

The mutant was cultivated in the medium E05. The strain was cultivatedat 28° C., 200 rpm in flasks and in a fermentor of 200 L working volumeusing aeration of 0.5 vvm, agitation 250 rpm and at 28° C. One seedcultivation was made to enhance cell mass for 200-l cultivation with theinoculation rate of 10%. After eight days cultivation either in flask orfermentor, the whole culture broth obtained was extracted withmethanol:chloroform (2:8) for 2 h at RT by shaking. The chloroform phasecontaining lipid fraction was studied by TLC for the amount of lipidsand 20 g/l as the minimum was detected. The efficiency of conversion ofpure glucose or glucose (20 g/l) derived from starch (40 g/l) is 33%.The amount of TAGs was in the range of 80-90% of all lipids. The cellmass was relatively low giving a low PMV value of 10-20% in the end ofcultivation.

GC analysis revealed that the lipid profile was characteristic toStreptomyces strain.

Example 15 Characterizations of the GMO-Strains

The strain characterization was carried out by the studies on colonymorphology, cycle time and production of metabolites.

PCR products used to construct GMO strains were verified by sequencing.Plasmids of the strains were isolated and digested to verify transformedplasmids.

The strains characters on ISP4 and ISP2 agar plates and in submergedcultivations in TSB and in E05 with waste variants are given here.

G009 is a Streptomyces albus GAL1001 strain carrying pIJEsco0958 anddesignated as clone 2. It does not produce detectable quantities ofbioactive metabolites and like GAL1001 it is suggested to be blocked inbiosynthesis of bioactive secondary metabolites due to a randommutation. Colony morphology: On ISP4 agar G009 form spores with whitepigment while in the reverse side of agar plate; the colonies are brownsurrounding by a thin bright zone. In a rich agar, ISP2, G009 coloniesform yellow substrate mycelia and yellowish aerial hyphae. Spores ofwhite pigment are slightly visible. Typical morphology in submergedculture is pellet or dispersed mycelia. The strain forms spores also insubmerged cultivations e.g. in TSB and in E05. The relevant charactersaccording to this disclosure are increased cell mass as compared to theparent strain and accumulation of TAGs in a variety of cultivationcondition up to 30 g/l. The characters of the strain are stabile inpassages up to 20 times tested so far.

G013 is a Streptomyces albus GAL1001 strain carrying pIJEsco5888. Itdoes not produce detectable quantities of bioactive metabolites and likeGAL1001 it is suggested to be blocked in biosynthesis of bioactivesecondary metabolites due to a random mutation. Colony morphology onsolid—and submerged cultivations is very similar to that described forG009 though the growth is not as good as found by G009. The colony sizeis somewhat smaller than found in G009 cultures on solid agar. Therelevant character according to this disclosure is accumulation of TAGsin a variety of cultivation condition up to 11 g/l.

G016 is a Streptomyces albus GAL1001 strain carrying pHJLsco5888. Itdoes not produce detectable quantities of bioactive metabolites and likeGAL1001 it is suggested to be blocked in biosynthesis of bioactivesecondary metabolites due to a random mutation. Colony morphology onsolid and submerged cultivations is very similar to that described forG009 though the growth is not as good as found by G009 but slightlybetter than found by G013. The relevant character according to thisdisclosure is accumulation of TAGs in a variety of cultivation conditionup to 24 g/l.

G011 is a mutant of GAL4111 and does not produce detectable quantitiesof bioactive metabolites characteristic to its parent strain. GAL4111has been identified to be Streptomyces roseosporus based on identicalpatterns of DNA sequence, colony characteristics and ability to producesmall quantities, some milligrams per litre of Daptomycin analogues.Colony morphology: On ISP4 agar G011 form spores with white/red pigmentwhile in the reverse side of agar plate, the substrate mycelia is fromreddish to brown and a thin clear zone around these red/brown coloniesis visible indicating an amylase activity. In a rich agar, ISP2, G011colonies are brown, slight sporulation with white/red pigment is seen.The substrate mycelia on ISP2 are slightly red with brownish aerialhyphae. In submerged cultivations it provides reddish pellet ordispersed mycelia. The strain forms spores also in submergedcultivations e.g. in TSB and in E05. The relevant characters accordingto this disclosure are increased cell mass as compared to the parentstrain and accumulation of TAGs 1 g/l.

G012 is a Streptomyces roseosporus G011 strain carrying pIJEsco0958 anddoes not produce detectable quantities of bioactive metabolites like itsparent strain G011. Colony morphology is identical to that described forG011. The growth is not, however, as good as found by G011. The colonysize is somewhat smaller than found in G011 cultures on solid agar whilethe colonies could be not distinguished based on that. The relevantcharacter according to this disclosure is accumulation of TAGs 12 g/l.

G017 is a Streptomyces roseosporus G011 strain carrying pHJLsco0958+5888and does not produce detectable quantities of bioactive metabolites likeits parent strain G011. Colony morphology is identical to that describedfor G011. The growth is very similar to that found by G011, The relevantcharacters according to this disclosure are increased cell mass ascompared to the parent strain and accumulation of TAGs 20 g/l.

G019 is a Streptomyces roseosporus G011 strain carrying pHJLsco5888 anddoes not produce detectable quantities of bioactive metabolites similarto its parent strain G011. Colony morphology is identical to thatdescribed for G011. The growth is very similar to that found by G011.The relevant characters according to this disclosure are increased cellmass as compared to the control strain GAL4111 and accumulation of TAGs17 g/l.

3010 is a Streptomyces roseosporus GAL4111 strain carrying pIJEsco0958and does not produce detectable quantities of bioactive metabolitesdissimilar to its parent strain GAL4111. Colony morphology is identicalto that described for G011. The growth is not, however, as good as foundby G011. The relevant character according to this disclosure isaccumulation of TAGs 18 g/l.

G014 is a Streptomyces roseosporus GAL4111 strain carrying pIJEsco5888and does not produce detectable quantities of bioactive metabolitesdissimilar to its parent strain GAL4111. Colony morphology is identicalto that described for G011. The growth is very similar to that found byG011. The relevant characters according to this disclosure are increasedcell mass as compared to the parent strain GAL4111 and accumulation ofTAGs 20 g/l like G017.

G015 is a Streptomyces roseosporus GAL4111 strain carryingpIJEsco5888+0958 and does not produce detectable quantities of bioactivemetabolites dissimilar to its parent strain GAL4111. Colony morphologyis identical to that described for G011. The growth rate is very similarto that found by G011. The relevant characters according to thisdisclosure are increased cell mass as compared to the parent strainGAL4111 and accumulation of TAGs 25 g/l.

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1. A process for producing lipids for biofuel or lubricant, whichcomprises cultivating bacterial cells of the genus Streptomyces in amedium comprising organic waste(s) or residue(s) or mixtures thereof ascarbon and/or nutrient source(s); recovering the lipids from the cellsor from the culture medium.
 2. The process according to claim 1, whereinthe organic waste(s) or residue(s) or mixtures thereof are the mainsource(s) of carbon and/or nutrient(s) in the cultivation medium.
 3. Theprocess according to claim 1, wherein the organic waste(s) or residue(s)comprise(s) industrial organic waste(s) or residue(s), agriculturalorganic waste(s) or residue(s), municipal waste(s) or microbial waste(s)or residue(s), or any mixtures thereof.
 4. The process according toclaim 1, wherein the cultivation medium comprises as an additionalcarbon source glycerol, a fraction from sugar or starch industry, sugaror starch syrup(s) or purified sugar(s) or any mixtures thereof.
 5. Theprocess according to claim 1, wherein the amount of triacylglycerols inthe spent culture medium is at least 1 g/litre, preferably at least 5g/litre.
 6. The process according to claim 1, wherein the producedlipids comprise mainly triacylglycerols.
 7. The process according toclaim 1, wherein the produced lipids are trans-esterified to producebiodiesel or hydrogen treated to produce renewable diesel.
 8. Theprocess according to claim 1, wherein the cultivation medium is notsterilized or is pasteurized.
 9. The process according to claim 1,wherein the cultivation medium comprises lipase inhibitors.
 10. Theprocess according to claim 1, wherein the cultivation is carried out asa batch or as a fed-batch fermentation.
 11. The process according toclaim 1, wherein the Streptomyces species is selected from the group ofStreptomyces roseosporus, Streptomyces griseus, Streptomyces albus,Streptomyces peucetius, Streptomyces aureofaciens, Streptomyceslividans, Streptomyces coelicolor, Streptomyces hygroscopicus,Streptomyces avermitilis, Streptomyces milbemycinius and Streptomyceslydicus.
 12. The process according to claim 1, wherein the Streptomyceshost is genetically modified to express at least one gene of the lipidsynthesis pathway.
 13. The process according to claim 1, wherein theStreptomyces host is genetically modified to express an endogenous orexogenous gene encoding DGAT (EC 2.3.1.20) and/or 3-ketoacyl-acylcarrier protein synthase III (FabH) (EC: 2.3.1.4.1).
 14. The processaccording to claim 1, wherein the Streptomyces host is geneticallymodified to express one or more of genes selected from the group of (a)sco0958 (SEQ ID NO:1) and/or sco5888 (SEQ ID NO:2); (b) the closesthomologue of said genes in a Streptomyces species; (c) a nucleotidesequence which hybridizes to at least one of said genes or saidhomologues under stringent hybridization conditions; (d) a nucleotidesequence causing the same or an equivalent function as gene products ID101096381 or ID 101101330 have; (e) a nucleotide sequence encoding anamino acid sequence showing at least 60% identity to SEQ ID NO: 3 or SEQID NO:4.
 15. The process according to claim 1, wherein the Streptomyceshost is made deficient in producing bioactive metabolites, such asantibiotic agents.
 16. A Streptomyces culture for lipid production,which comprises (a) a population of bacteria of the genus Streptomyces;and (b) a culture medium comprising organic waste(s) or residue(s) ormixtures thereof as carbon and/or nutrient source(s).
 17. The cultureaccording to claim 16, wherein the organic waste(s) or residue(s) ormixtures thereof are the main source(s) of carbon and/or nutrient(s) inthe cultivation medium.
 18. The culture according to claim 16, whereinthe amount of triacylglycerols in the spent culture medium is at least 1g/litre, preferably at least 5 g/litre.
 19. The process according toclaim 16, wherein the produced lipid fraction comprises mainlytriacylglycerols.
 20. The culture according to claim 16, wherein thecultivation medium comprises lipase inhibitors.
 21. The cultureaccording to claim 16, wherein the cultivation medium is not sterilizedor is pasteurized.
 22. The culture according to claim 16, wherein theStreptomyces species is selected from the group of Streptomycesroseosporus, Streptomyces griseus, Streptomyces albus, Streptomycespeucetius, Streptomyces aureofaciens Streptomyces lividans, Streptomycescoelicolor, Streptomyces hygroscopicus, Streptomyces avermitilis,Streptomyces milbemycinius and Streptomyces lydicus, preferably from thegroup of Streptomyces roseosporus, Streptomyces griseus, Streptomycesalbus, Streptomyces peucetius, Streptomyces aureofaciens andStreptomyces milbemycinius.
 23. The culture according to claim 16,wherein the Streptomyces host is genetically modified to express atleast one gene of the lipid synthesis pathway.
 24. The culture accordingto claim 16, wherein the Streptomyces host is genetically modified toexpress an endogenous or exogenous gene encoding DGAT (EC 2.3.1.20)and/or 3-ketoacyl-acyl carrier protein synthase III (FabH) (EC:2.3.1.41).
 25. The culture according to claim 16, wherein theStreptomyces host is genetically modified to express one or more ofgenes selected from the group of (a) sco0958 (SEC) ID NO:1) and/orsco5888 (SEQ ID NO:2); (b) the closest homologue of said genes in aStreptomyces species; (c) a nucleotide sequence which hybridizes to atleast one of said genes or said homologues under stringent hybridizationconditions; (d) a nucleotide sequence causing the same or an equivalentfunction as gene products ID 101096381 or ID 101101330 have; (e) anucleotide sequence encoding an amino acid sequence showing at least 60%identity to SEQ ID NO: 3 or SEQ ID NO:4.
 26. The culture according toclaim 16, wherein the Streptomyces host is deficient in producingbioactive metabolites, such as antibiotic agents.
 27. A Streptomyceshost genetically modified to express an endogenous or exogenous geneencoding DGAT activity (EC 2.3.1.20) and/or 3-ketoacyl-acyl carrierprotein synthase III (FabH) (EC: 2.3.1.41), or a nucleotide sequencecausing the same or an equivalent function as gene products ID 101096381or ID 101101330 have.
 28. The host according to claim 27, wherein thehost cell is selected from the group of species Streptomycesroseosporus, Streptomyces griseus, Streptomyces albus, Streptomycespeucetius, Streptomyces aureofaciens, Streptomyces lividans,Streptomyces hygroscopicus, Streptomyces avermitilis, Streptomyceslydicus, and Streptomyces milbemycinius, preferably selected from thegroup of species Streptomyces roseosporus, Streptomyces milbemyciniusand Streptomyces albus.
 29. The host according to claim 27, wherein thehost is genetically modified to express one or more of genes selectedfrom the group of (a) sco0958 (SEQ ID NO:1) and/or sco5888 (SEQ IDNO:2); (b) the closest homologue of said genes in a Streptomycesspecies; (c) a nucleotide sequence which hybridizes to at least one ofsaid genes or said homologues under stringent hybridization conditions;(d) a nucleotide sequence causing the same or an equivalent function asgene products ID 101096381 or ID 101101330 have; (e) a nucleotidesequence encoding an amino acid sequence showing at least 60% identityto SEQ ID NO: 3 or SEQ ID NO:4.
 30. A lipid composition producedaccording to claim
 1. 31. Use of the lipids or lipid compositionobtained according to claim 1, or a fraction of the lipids or lipidcomposition as biofuel and/or lubricant, or as a starting material forbiofuel and/or lubricant production.
 32. Use of the lipids or lipidcomposition obtained according to claim 1, for the production ofbiodiesel or renewable diesel.
 33. Biofuel which comprises the lipids orlipid composition obtained according to claim 1, or a fraction of lipidsor lipid composition, and optionally suitable additives for biofuel use.34. Lubricant which comprises the lipids or lipid composition obtainedaccording to claim 1, or a fraction of lipids or lipid composition, andoptionally suitable additives for lubricant use.